diff --git a/examples/colin27/createmesh.m b/examples/colin27/createmesh.m
index d56cbf14..6e6bd390 100644
--- a/examples/colin27/createmesh.m
+++ b/examples/colin27/createmesh.m
@@ -1,11 +1,11 @@
-addpath('../../../matlab/'); 
+addpath('../../../matlab/');
 
-if(~exist('MMC_Collins_Atlas_Mesh_Version_2L.mat','file'))
-     f=websave('MMC_Collins_Atlas_Mesh_Version_2L.mat','https://github.com/fangq/Colin27BrainMesh/raw/master/MMC_Collins_Atlas_Mesh_Version_2L.mat');
-     if(~exist('MMC_Collins_Atlas_Mesh_Version_2L.mat','file'))
-          warning('Please download Colin27 atlas mesh from https://github.com/fangq/Colin27BrainMesh/raw/master/MMC_Collins_Atlas_Mesh_Version_2L.mat')
-     end
+if (~exist('MMC_Collins_Atlas_Mesh_Version_2L.mat', 'file'))
+    f = websave('MMC_Collins_Atlas_Mesh_Version_2L.mat', 'https://github.com/fangq/Colin27BrainMesh/raw/master/MMC_Collins_Atlas_Mesh_Version_2L.mat');
+    if (~exist('MMC_Collins_Atlas_Mesh_Version_2L.mat', 'file'))
+        warning('Please download Colin27 atlas mesh from https://github.com/fangq/Colin27BrainMesh/raw/master/MMC_Collins_Atlas_Mesh_Version_2L.mat');
+    end
 end
 
-load MMC_Collins_Atlas_Mesh_Version_2L.mat
-savemmcmesh('brain',node,elem);
+load MMC_Collins_Atlas_Mesh_Version_2L.mat;
+savemmcmesh('brain', node, elem);
diff --git a/examples/dcs/createmesh.m b/examples/dcs/createmesh.m
index a01194d3..b84a9bbf 100644
--- a/examples/dcs/createmesh.m
+++ b/examples/dcs/createmesh.m
@@ -1,10 +1,9 @@
-addpath ../../matlab
-srcpos=[50.5 50.5 0];
+addpath ../../matlab;
+srcpos = [50.5 50.5 0];
 fprintf('Generating mesh...');
-[node,elem] = genT5mesh(0:4:100,0:4:100,0:4:80);
+[node, elem] = genT5mesh(0:4:100, 0:4:100, 0:4:80);
 fprintf('done\nSaving mesh..');
-savemmcmesh('dcs',node(:,1:3),elem); % 4th column of node is label and confuses savemmcmesh volume calculation
+savemmcmesh('dcs', node(:, 1:3), elem); % 4th column of node is label and confuses savemmcmesh volume calculation
 fprintf('done\nFinding element enclosing source: ');
-eid=tsearchn(node(:,1:3),elem(:,1:4),srcpos);
-fprintf('%d\n',eid);
-
+eid = tsearchn(node(:, 1:3), elem(:, 1:4), srcpos);
+fprintf('%d\n', eid);
diff --git a/examples/dcs/dcs_example.m b/examples/dcs/dcs_example.m
index 899554c9..45f14540 100644
--- a/examples/dcs/dcs_example.m
+++ b/examples/dcs/dcs_example.m
@@ -1,38 +1,40 @@
 addpath('../../matlab');
 
-Db=1e-7; % simulated brownian motion diffusion coefficient
-sim_beta=0.4;
+Db = 1e-7; % simulated brownian motion diffusion coefficient
+sim_beta = 0.4;
 
-mua=0.01;
-mus=1;
-g=0.01;
-musp=mus*(1-g);
-sdsep=15;
-prob_scat_moving_scat=1;
+mua = 0.01;
+mus = 1;
+g = 0.01;
+musp = mus * (1 - g);
+sdsep = 15;
+prob_scat_moving_scat = 1;
 
-
-[tau,g1]=generate_g1('dcs.mch',logspace(-8,0,200),'brownian',Db);
+[tau, g1] = generate_g1('dcs.mch', logspace(-8, 0, 200), 'brownian', Db);
 
 figure(1);
-for I=1:4,
-    subplot(2,2,I); 
-    semilogx(tau,g1(I,:),'.');
-    x=fminsearch(@(x) dcs_g1_Db_fms(x,tau,g1(I,:),sdsep,mua,musp,prob_scat_moving_scat),[1e-5]);
+for I = 1:4
+    subplot(2, 2, I);
+    semilogx(tau, g1(I, :), '.');
+    x = fminsearch(@(x) dcs_g1_Db_fms(x, tau, g1(I, :), sdsep, mua, musp, prob_scat_moving_scat), [1e-5]);
     hold on;
-    semilogx(tau,dcs_g1_Db(x,tau,sdsep,mua,musp,prob_scat_moving_scat),'r');
-    xlabel('\tau (s)'); ylabel('g_1(\tau)');axis tight;
-    title(['Det ' num2str(I) ': fit Db: ' sprintf('%.2g',x) ' err: ' num2str((x-Db)/Db*100,'%.1f') '%']);
+    semilogx(tau, dcs_g1_Db(x, tau, sdsep, mua, musp, prob_scat_moving_scat), 'r');
+    xlabel('\tau (s)');
+    ylabel('g_1(\tau)');
+    axis tight;
+    title(['Det ' num2str(I) ': fit Db: ' sprintf('%.2g', x) ' err: ' num2str((x - Db) / Db * 100, '%.1f') '%']);
 end
 
-figure(2); 
-for I=1:4,
-    subplot(2,2,I); 
-    g2=1+sim_beta*g1(I,:).^2;
-    semilogx(tau,g2,'.');
-    x=fminsearch(@(x) dcs_g2_Db_fms(x,tau,g2,sdsep,mua,musp,prob_scat_moving_scat),[1e-5 0.5]);
+figure(2);
+for I = 1:4
+    subplot(2, 2, I);
+    g2 = 1 + sim_beta * g1(I, :).^2;
+    semilogx(tau, g2, '.');
+    x = fminsearch(@(x) dcs_g2_Db_fms(x, tau, g2, sdsep, mua, musp, prob_scat_moving_scat), [1e-5 0.5]);
     hold on;
-    semilogx(tau,dcs_g2_Db(x(1),tau,sdsep,mua,musp,prob_scat_moving_scat,x(2)),'r');
-    xlabel('\tau (s)'); ylabel('g_2(\tau)');axis tight;
-    title(['Det ' num2str(I) ': fit Db: ' sprintf('%.2g',x(1)) ' err: ' num2str((x(1)-Db)/Db*100,'%.1f') '%']);
+    semilogx(tau, dcs_g2_Db(x(1), tau, sdsep, mua, musp, prob_scat_moving_scat, x(2)), 'r');
+    xlabel('\tau (s)');
+    ylabel('g_2(\tau)');
+    axis tight;
+    title(['Det ' num2str(I) ': fit Db: ' sprintf('%.2g', x(1)) ' err: ' num2str((x(1) - Db) / Db * 100, '%.1f') '%']);
 end
-
diff --git a/examples/dcs/dcs_g1_Db.m b/examples/dcs/dcs_g1_Db.m
index edcbec97..275f5199 100644
--- a/examples/dcs/dcs_g1_Db.m
+++ b/examples/dcs/dcs_g1_Db.m
@@ -1,16 +1,18 @@
-function result=dcs_g1_Db(Db,tau,sdsep,mu_a,mu_sp,alpha)
-% 
+function result = dcs_g1_Db(Db, tau, sdsep, mu_a, mu_sp, alpha)
+%
 % this function generates analytical auto-correlation decay for a semi-
 % infinite medium
 %
 % sdsep, mu_a and mu_sp units must be mm
 
-zo=(mu_sp+mu_a)^-1; zb= 1.76/mu_sp; % this assumes n_tissue=1.35
-r1=(sdsep^2+zo^2)^(1/2); r2=(sdsep^2+(zo+2*zb)^2)^(1/2); 
-k0=2*pi*1.35/(785*1e-6); %wavelength=786e-6 mm!
-kd=(3*mu_sp*mu_a+mu_sp^2*k0^2*alpha.*(6*Db.*tau)).^(1/2);
-kd0=(3*mu_sp*mu_a).^(1/2);
-fit_g1=exp(-kd.*r1)/r1-exp(-kd.*r2)/r2;
-fit_g1_norm=exp(-kd0.*r1)/r1-exp(-kd0.*r2)/r2;
+zo = (mu_sp + mu_a)^-1;
+zb = 1.76 / mu_sp; % this assumes n_tissue=1.35
+r1 = (sdsep^2 + zo^2)^(1 / 2);
+r2 = (sdsep^2 + (zo + 2 * zb)^2)^(1 / 2);
+k0 = 2 * pi * 1.35 / (785 * 1e-6); % wavelength=786e-6 mm!
+kd = (3 * mu_sp * mu_a + mu_sp^2 * k0^2 * alpha .* (6 * Db .* tau)).^(1 / 2);
+kd0 = (3 * mu_sp * mu_a).^(1 / 2);
+fit_g1 = exp(-kd .* r1) / r1 - exp(-kd .* r2) / r2;
+fit_g1_norm = exp(-kd0 .* r1) / r1 - exp(-kd0 .* r2) / r2;
 
-result=fit_g1/fit_g1_norm;
\ No newline at end of file
+result = fit_g1 / fit_g1_norm;
diff --git a/examples/dcs/dcs_g1_Db_fms.m b/examples/dcs/dcs_g1_Db_fms.m
index f25db66f..6ba34924 100644
--- a/examples/dcs/dcs_g1_Db_fms.m
+++ b/examples/dcs/dcs_g1_Db_fms.m
@@ -1,16 +1,18 @@
-function result=dcs_g1_Db_fms(Db,tau,g1,sdsep,mu_a,mu_sp,alpha)
-% 
+function result = dcs_g1_Db_fms(Db, tau, g1, sdsep, mu_a, mu_sp, alpha)
+%
 % this function generates analytical auto-correlation decay for a semi-
 % infinite medium, and computes the rms error for fminsearch fitting
 %
 % sdsep, mu_a and mu_sp units must be mm
 
-zo=(mu_sp+mu_a)^-1; zb= 1.76/mu_sp; % this assumes n_tissue=1.35
-r1=(sdsep^2+zo^2)^(1/2); r2=(sdsep^2+(zo+2*zb)^2)^(1/2); 
-k0=2*pi*1.35/(785*1e-6); %wavelength=786e-6 mm!
-kd=(3*mu_sp*mu_a+mu_sp^2*k0^2*alpha.*(6*Db.*tau)).^(1/2);
-kd0=(3*mu_sp*mu_a).^(1/2);
-fit_g1=exp(-kd.*r1)/r1-exp(-kd.*r2)/r2;
-fit_g1_norm=exp(-kd0.*r1)/r1-exp(-kd0.*r2)/r2;
+zo = (mu_sp + mu_a)^-1;
+zb = 1.76 / mu_sp; % this assumes n_tissue=1.35
+r1 = (sdsep^2 + zo^2)^(1 / 2);
+r2 = (sdsep^2 + (zo + 2 * zb)^2)^(1 / 2);
+k0 = 2 * pi * 1.35 / (785 * 1e-6); % wavelength=786e-6 mm!
+kd = (3 * mu_sp * mu_a + mu_sp^2 * k0^2 * alpha .* (6 * Db .* tau)).^(1 / 2);
+kd0 = (3 * mu_sp * mu_a).^(1 / 2);
+fit_g1 = exp(-kd .* r1) / r1 - exp(-kd .* r2) / r2;
+fit_g1_norm = exp(-kd0 .* r1) / r1 - exp(-kd0 .* r2) / r2;
 
-result=sum((g1-fit_g1/fit_g1_norm).^2);
\ No newline at end of file
+result = sum((g1 - fit_g1 / fit_g1_norm).^2);
diff --git a/examples/dcs/dcs_g2_Db.m b/examples/dcs/dcs_g2_Db.m
index dd50b0a7..473bb9e4 100644
--- a/examples/dcs/dcs_g2_Db.m
+++ b/examples/dcs/dcs_g2_Db.m
@@ -1,19 +1,20 @@
-function g2=dcs_g2_Db(Db,tau,sdsep,mu_a,mu_sp,alpha,beta)
-% 
+function g2 = dcs_g2_Db(Db, tau, sdsep, mu_a, mu_sp, alpha, beta)
+%
 % this function generates analytical field auto-correlation decay for a semi-
 % infinite medium, then uses the Siegert relationship to derive the
 % intensity temporal auto-correlation decay assuming ergodicity
 %
 % sdsep, mu_a and mu_sp units must be mm
 
-zo=(mu_sp+mu_a)^-1; zb= 1.76/mu_sp; % this assumes n_tissue=1.35
-r1=(sdsep^2+zo^2)^(1/2); r2=(sdsep^2+(zo+2*zb)^2)^(1/2); 
-k0=2*pi*1.35/(785*1e-6); %wavelength=786e-6 mm!
-kd=(3*mu_sp*mu_a+mu_sp^2*k0^2*alpha.*(6*Db.*tau)).^(1/2);
-kd0=(3*mu_sp*mu_a).^(1/2);
-fit_g1=exp(-kd.*r1)/r1-exp(-kd.*r2)/r2;
-fit_g1_norm=exp(-kd0.*r1)/r1-exp(-kd0.*r2)/r2;
-
-g1_norm=fit_g1/fit_g1_norm;
-g2=1+beta*(g1_norm).^2;
+zo = (mu_sp + mu_a)^-1;
+zb = 1.76 / mu_sp; % this assumes n_tissue=1.35
+r1 = (sdsep^2 + zo^2)^(1 / 2);
+r2 = (sdsep^2 + (zo + 2 * zb)^2)^(1 / 2);
+k0 = 2 * pi * 1.35 / (785 * 1e-6); % wavelength=786e-6 mm!
+kd = (3 * mu_sp * mu_a + mu_sp^2 * k0^2 * alpha .* (6 * Db .* tau)).^(1 / 2);
+kd0 = (3 * mu_sp * mu_a).^(1 / 2);
+fit_g1 = exp(-kd .* r1) / r1 - exp(-kd .* r2) / r2;
+fit_g1_norm = exp(-kd0 .* r1) / r1 - exp(-kd0 .* r2) / r2;
 
+g1_norm = fit_g1 / fit_g1_norm;
+g2 = 1 + beta * (g1_norm).^2;
diff --git a/examples/dcs/dcs_g2_Db_fms.m b/examples/dcs/dcs_g2_Db_fms.m
index 3e8b3934..72d3aedb 100644
--- a/examples/dcs/dcs_g2_Db_fms.m
+++ b/examples/dcs/dcs_g2_Db_fms.m
@@ -1,23 +1,25 @@
-function result=dcs_g2_Db_fms(s,tau,g2,sdsep,mu_a,mu_sp,alpha)
-% 
+function result = dcs_g2_Db_fms(s, tau, g2, sdsep, mu_a, mu_sp, alpha)
+%
 % this function generates analytical field auto-correlation decay for a semi-
 % infinite medium, then uses the Siegert relationship to derive the
 % intensity temporal auto-correlation decay assuming ergodicity
 %
 % sdsep, mu_a and mu_sp units must be mm
 
-Db=s(1);
-beta=s(2);
+Db = s(1);
+beta = s(2);
 
-zo=(mu_sp+mu_a)^-1; zb= 1.76/mu_sp; % this assumes n_tissue=1.35
-r1=(sdsep^2+zo^2)^(1/2); r2=(sdsep^2+(zo+2*zb)^2)^(1/2); 
-k0=2*pi*1.35/(785*1e-6); %wavelength=786e-6 mm!
-kd=(3*mu_sp*mu_a+mu_sp^2*k0^2*alpha.*(6*Db.*tau)).^(1/2);
-kd0=(3*mu_sp*mu_a).^(1/2);
-fit_g1=exp(-kd.*r1)/r1-exp(-kd.*r2)/r2;
-fit_g1_norm=exp(-kd0.*r1)/r1-exp(-kd0.*r2)/r2;
+zo = (mu_sp + mu_a)^-1;
+zb = 1.76 / mu_sp; % this assumes n_tissue=1.35
+r1 = (sdsep^2 + zo^2)^(1 / 2);
+r2 = (sdsep^2 + (zo + 2 * zb)^2)^(1 / 2);
+k0 = 2 * pi * 1.35 / (785 * 1e-6); % wavelength=786e-6 mm!
+kd = (3 * mu_sp * mu_a + mu_sp^2 * k0^2 * alpha .* (6 * Db .* tau)).^(1 / 2);
+kd0 = (3 * mu_sp * mu_a).^(1 / 2);
+fit_g1 = exp(-kd .* r1) / r1 - exp(-kd .* r2) / r2;
+fit_g1_norm = exp(-kd0 .* r1) / r1 - exp(-kd0 .* r2) / r2;
 
-g1_norm=fit_g1/fit_g1_norm;
-fit_g2=1+beta*(g1_norm).^2;
+g1_norm = fit_g1 / fit_g1_norm;
+fit_g2 = 1 + beta * (g1_norm).^2;
 
-result=sum((g2-fit_g2).^2);
+result = sum((g2 - fit_g2).^2);
diff --git a/examples/mcxsph/createmcxbin.m b/examples/mcxsph/createmcxbin.m
index b354e03c..487fcd8c 100644
--- a/examples/mcxsph/createmcxbin.m
+++ b/examples/mcxsph/createmcxbin.m
@@ -1,11 +1,11 @@
-dim=60;
-[xi,yi,zi]=meshgrid(1:dim,1:dim,1:dim);
-dist=(xi-30).^2+(yi-30).^2+(zi-30).^2;
+dim = 60;
+[xi, yi, zi] = meshgrid(1:dim, 1:dim, 1:dim);
+dist = (xi - 30).^2 + (yi - 30).^2 + (zi - 30).^2;
 
-v=zeros(size(xi));
-v(dist<100)=1;
-v=v+1;
+v = zeros(size(xi));
+v(dist < 100) = 1;
+v = v + 1;
 
-fid=fopen('spherebox.bin','wb');
-aa=fwrite(fid,v,'uchar');
+fid = fopen('spherebox.bin', 'wb');
+aa = fwrite(fid, v, 'uchar');
 fclose(fid);
diff --git a/examples/meshtest/createmesh.m b/examples/meshtest/createmesh.m
index bdee2936..b3bd9c18 100644
--- a/examples/meshtest/createmesh.m
+++ b/examples/meshtest/createmesh.m
@@ -4,66 +4,64 @@
 
 % preparation
 
-% 1. you need to add the path to iso2mesh toolbox 
+% 1. you need to add the path to iso2mesh toolbox
 % addpath('/path/to/iso2mesh/toolbox/');
 
 % 2. you need to add the path to MMC matlab folder
-addpath('../../matlab')
-
+addpath('../../matlab');
 
 % create a surface mesh for a 10mm radius sphere
-[no,el]=meshasphere([30 30 30],10,1.0);
-
+[no, el] = meshasphere([30 30 30], 10, 1.0);
 
 % generate a coarse volumetric mesh from the sphere with an additional bounding box
 % the maximum element volume is 20
 
-ISO2MESH_SESSION='mmcmesh2_';
+ISO2MESH_SESSION = 'mmcmesh2_';
 
-srcpos=[30. 30. 0.];
-fixednodes=[30.,30.,0.05; 30 30 30];
-nodesize=[ones(size(no,1),1) ; 0.5; 3];
-nfull=[no;fixednodes];
-[node3,elem3,face3]=surf2mesh([nfull,nodesize],el,[0 0 0],[60.1 60.1 60.1],1,8,[30 30 30],[],[1.5 1.5 1.5 1.5 5 5 5 5]);
-[node3,elem3]=sortmesh(srcpos,node3,elem3,1:4);
-elem3(:,1:4)=meshreorient(node3,elem3(:,1:4));
-elem3(:,5)=elem3(:,5)+1;
-savemmcmesh('mesh2',node3,elem3(:,1:5),[]);
-eid3=tsearchn(node3,elem3(:,1:4),srcpos);
+srcpos = [30. 30. 0.];
+fixednodes = [30., 30., 0.05; 30 30 30];
+nodesize = [ones(size(no, 1), 1); 0.5; 3];
+nfull = [no; fixednodes];
+[node3, elem3, face3] = surf2mesh([nfull, nodesize], el, [0 0 0], [60.1 60.1 60.1], 1, 8, [30 30 30], [], [1.5 1.5 1.5 1.5 5 5 5 5]);
+[node3, elem3] = sortmesh(srcpos, node3, elem3, 1:4);
+elem3(:, 1:4) = meshreorient(node3, elem3(:, 1:4));
+elem3(:, 5) = elem3(:, 5) + 1;
+savemmcmesh('mesh2', node3, elem3(:, 1:5), []);
+eid3 = tsearchn(node3, elem3(:, 1:4), srcpos);
 
 % generate a dense volumetric mesh from the sphere with an additional bounding box
 % the maximum element volume is 5
 
-ISO2MESH_SESSION='mmcmesh1_';
+ISO2MESH_SESSION = 'mmcmesh1_';
 
-nodesize=[1*ones(size(no,1),1) ; 1; 1];
-[node2,elem2,face2]=surf2mesh([nfull,nodesize],el,[0 0 0],[60.1 60.1 60.1],1,2,[30 30 30],[],[1 1 1 1 1 1 1 1]);
-[node2,elem2]=sortmesh(srcpos,node2,elem2,1:4);
-elem2(:,1:4)=meshreorient(node2,elem2(:,1:4));
-elem2(:,5)=elem2(:,5)+1;
-savemmcmesh('mesh1',node2,elem2(:,1:5),[]);
-eid2=tsearchn(node2,elem2(:,1:4),srcpos);
+nodesize = [1 * ones(size(no, 1), 1); 1; 1];
+[node2, elem2, face2] = surf2mesh([nfull, nodesize], el, [0 0 0], [60.1 60.1 60.1], 1, 2, [30 30 30], [], [1 1 1 1 1 1 1 1]);
+[node2, elem2] = sortmesh(srcpos, node2, elem2, 1:4);
+elem2(:, 1:4) = meshreorient(node2, elem2(:, 1:4));
+elem2(:, 5) = elem2(:, 5) + 1;
+savemmcmesh('mesh1', node2, elem2(:, 1:5), []);
+eid2 = tsearchn(node2, elem2(:, 1:4), srcpos);
 
 % reduce the surface node numbers to 20%
 
-ISO2MESH_SESSION='mmcmesh0_';
+ISO2MESH_SESSION = 'mmcmesh0_';
 
-%[no2,el2]=meshresample(no,el,0.2);
+% [no2,el2]=meshresample(no,el,0.2);
 
 % using the coarse spherical surface, we generate a coarse volumetric
 % mesh with maximum volume of 10
 
-nodesize=[ones(size(no,1),1); 3];
-nfull=[no; 30 30 30];
-[node1,elem1,face1]=surf2mesh([nfull,nodesize],el,[0 0 0],[60.1 60.1 60.1],1,10,[30 30 30],[],[2 2 2 2 5 5 5 5]);
-[node1,elem1]=sortmesh(srcpos,node1,elem1,1:4);
-elem1(:,1:4)=meshreorient(node1,elem1(:,1:4));
-elem1(:,5)=elem1(:,5)+1;
-savemmcmesh('mesh0',node1,elem1(:,1:5),[]);
-eid1=tsearchn(node1,elem1(:,1:4),srcpos);
+nodesize = [ones(size(no, 1), 1); 3];
+nfull = [no; 30 30 30];
+[node1, elem1, face1] = surf2mesh([nfull, nodesize], el, [0 0 0], [60.1 60.1 60.1], 1, 10, [30 30 30], [], [2 2 2 2 5 5 5 5]);
+[node1, elem1] = sortmesh(srcpos, node1, elem1, 1:4);
+elem1(:, 1:4) = meshreorient(node1, elem1(:, 1:4));
+elem1(:, 5) = elem1(:, 5) + 1;
+savemmcmesh('mesh0', node1, elem1(:, 1:5), []);
+eid1 = tsearchn(node1, elem1(:, 1:4), srcpos);
 
-clear ISO2MESH_SESSION
+clear ISO2MESH_SESSION;
 
-fid=fopen('initial_elem.txt','wt');
-fprintf(fid,'mesh0: %d\nmesh1: %d\nmesh2: %d\n',eid1,eid2,eid3);
+fid = fopen('initial_elem.txt', 'wt');
+fprintf(fid, 'mesh0: %d\nmesh1: %d\nmesh2: %d\n', eid1, eid2, eid3);
 fclose(fid);
diff --git a/examples/meshtest/plotmmcsph.m b/examples/meshtest/plotmmcsph.m
index 552c2ed3..0c4f5aa3 100644
--- a/examples/meshtest/plotmmcsph.m
+++ b/examples/meshtest/plotmmcsph.m
@@ -1,157 +1,156 @@
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% add paths to the necessary toolboxes
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-addpath('/space/kwafoo/2/users/fangq/Projects/mcx/utils/')
-addpath('../../matlab')
+addpath('/space/kwafoo/2/users/fangq/Projects/mcx/utils/');
+addpath('../../matlab');
 
-c0=299792458000;
-t0=0;
-dt=1e-10;
-t1=5e-9;
+c0 = 299792458000;
+t0 = 0;
+dt = 1e-10;
+t1 = 5e-9;
 
-twin=[t0+dt/2:dt:t1];
-gates=length(twin);
-clines=[-1:0.5:8]-10;
+twin = [t0 + dt / 2:dt:t1];
+gates = length(twin);
+clines = [-1:0.5:8] - 10;
 
-[xi,yi]=meshgrid(1:60,0:60);
+[xi, yi] = meshgrid(1:60, 0:60);
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% load MCX results
-%%-----------------------------------------------------------------
-mcx=loadmc2('../mcxsph/spherebox.mc2', [60 60 60 gates]);
-cwmcx=sum(mcx,4)*dt;
+%% -----------------------------------------------------------------
+mcx = loadmc2('../mcxsph/spherebox.mc2', [60 60 60 gates]);
+cwmcx = sum(mcx, 4) * dt;
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% generate/load analytical solution for sphere inside infinite slab
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-%[phi_ana,xa,ya,za]=sphdiffusionslab(0,0,60,-22:0.8:22,0,-30:0.8:10);
-%save sphdiffsemiinf.mat phi_ana xa ya za
+% [phi_ana,xa,ya,za]=sphdiffusionslab(0,0,60,-22:0.8:22,0,-30:0.8:10);
+% save sphdiffsemiinf.mat phi_ana xa ya za
 
-load sphdiffsemiinf.mat
-idx=find((xa(:)<-12 | xa(:)>12) & za(:)>-5);
-phi_ana(idx)=nan;
-idx=find((xa(:)<-10 | xa(:)>10) & za(:)>0);
-phi_ana(idx)=nan;
+load sphdiffsemiinf.mat;
+idx = find((xa(:) < -12 | xa(:) > 12) & za(:) > -5);
+phi_ana(idx) = nan;
+idx = find((xa(:) < -10 | xa(:) > 10) & za(:) > 0);
+phi_ana(idx) = nan;
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% generate the contour of the inclusion
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-[xcirc,ycirc] = cylinder(10,200);
-xcirc=xcirc(1,:)+30;
-ycirc=ycirc(1,:)+30;
+[xcirc, ycirc] = cylinder(10, 200);
+xcirc = xcirc(1, :) + 30;
+ycirc = ycirc(1, :) + 30;
 
 % create the voxel-contour of the sphere for MCX
-%dim=60;
-%[xv,yv,zv]=meshgrid(1:dim,1:dim,1:dim);
-%dist=(xv-30).^2+(yv-30).^2+(zv-30).^2;
+% dim=60;
+% [xv,yv,zv]=meshgrid(1:dim,1:dim,1:dim);
+% dist=(xv-30).^2+(yv-30).^2+(zv-30).^2;
 
-%vv=zeros(size(xv));
-%vv(dist<100)=1;
+% vv=zeros(size(xv));
+% vv(dist<100)=1;
 
-%c=contourc(squeeze(vv(:,30,:)),1);
-%plot(c(1,2:end),c(2,2:end),'c--')
+% c=contourc(squeeze(vv(:,30,:)),1);
+% plot(c(1,2:end),c(2,2:end),'c--')
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% plot sphere 1
-%%-----------------------------------------------------------------
-node1=readmmcnode('node_mesh0.dat');  
-elem1=readmmcelem('elem_mesh0.dat');
-load mesh0.dat
-mesh0=reshape(mesh0(:,end),[size(node1,1),length(mesh0)/size(node1,1)]);
-s1=sum(mesh0,2)*dt;
-[cutpos,cutvalue,facedata]=qmeshcut(elem1(:,1:4),node1,s1,[0 30 0; 0 30 1; 1 30 0]);
-%patch('Vertices',cutpos,'Faces',facedata,'FaceVertexCData',log10(cutvalue),'FaceColor','interp','linestyle','none');
-%view([0 1 0])
-
-vi=griddata(cutpos(:,1),cutpos(:,3),cutvalue,xi,yi);
-
-figure
-hold on
-[cc,hc]=contour(xa+30,za+31,log10(abs(phi_ana)),clines,'color',[0.7 0.7 0.7],'linewidth',2);
-contour(log10(squeeze(abs(cwmcx(:,30,:)))'),clines,'b-')
-contour(log10(abs(vi)),clines,'r:')
-plot(xcirc,ycirc,'k--','linewidth',2);
-
-axis equal
-set(gca,'xlim',[1 60]);
-set(gca,'ylim',[1 60]);
-set(gca,'fontsize',18)
-xlabel('x (mm)')
-ylabel('z (mm)')
-legend('Diffusion','MCX','MMCM')
+%% -----------------------------------------------------------------
+node1 = readmmcnode('node_mesh0.dat');
+elem1 = readmmcelem('elem_mesh0.dat');
+load mesh0.dat;
+mesh0 = reshape(mesh0(:, end), [size(node1, 1), length(mesh0) / size(node1, 1)]);
+s1 = sum(mesh0, 2) * dt;
+[cutpos, cutvalue, facedata] = qmeshcut(elem1(:, 1:4), node1, s1, [0 30 0; 0 30 1; 1 30 0]);
+% patch('Vertices',cutpos,'Faces',facedata,'FaceVertexCData',log10(cutvalue),'FaceColor','interp','linestyle','none');
+% view([0 1 0])
+
+vi = griddata(cutpos(:, 1), cutpos(:, 3), cutvalue, xi, yi);
+
+figure;
+hold on;
+[cc, hc] = contour(xa + 30, za + 31, log10(abs(phi_ana)), clines, 'color', [0.7 0.7 0.7], 'linewidth', 2);
+contour(log10(squeeze(abs(cwmcx(:, 30, :)))'), clines, 'b-');
+contour(log10(abs(vi)), clines, 'r:');
+plot(xcirc, ycirc, 'k--', 'linewidth', 2);
+
+axis equal;
+set(gca, 'xlim', [1 60]);
+set(gca, 'ylim', [1 60]);
+set(gca, 'fontsize', 18);
+xlabel('x (mm)');
+ylabel('z (mm)');
+legend('Diffusion', 'MCX', 'MMCM');
 legend boxoff;
 box on;
-set(gcf,'PaperPositionMode','auto');
-print -depsc2 mesh0.eps
+set(gcf, 'PaperPositionMode', 'auto');
+print -depsc2 mesh0.eps;
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% plot sphere 2
-%%-----------------------------------------------------------------
-
-node2=readmmcnode('node_mesh1.dat');						    
-elem2=readmmcelem('elem_mesh1.dat');										    
-load mesh1.dat
-mesh1=reshape(mesh1(:,end),[size(node2,1),length(mesh1)/size(node2,1)]);
-s2=sum(mesh1,2)*dt;
-[cutpos,cutvalue,facedata]=qmeshcut(elem2(:,1:4),node2,s2,[0 30 0; 0 30 1; 1 30 0]);
-%patch('Vertices',cutpos,'Faces',facedata,'FaceVertexCData',log10(cutvalue),'FaceColor','interp','linestyle','none');
-%view([0 1 0])
-vi=griddata(cutpos(:,1),cutpos(:,3),cutvalue,xi,yi);
-
-figure
-hold on
-[cc,hc]=contour(xa+30,za+31,log10(abs(phi_ana)),clines,'color',[0.7 0.7 0.7],'linewidth',2);
-contour(log10(squeeze(abs(cwmcx(:,30,:)))'),clines,'b-')
-contour(log10(abs(vi)),clines,'r:')
-plot(xcirc,ycirc,'k--','linewidth',2);
-
-axis equal
-set(gca,'xlim',[1 60]);
-set(gca,'ylim',[1 60]);
-set(gca,'fontsize',18)
-xlabel('x (mm)')
-ylabel('z (mm)')
-legend('Diffusion','MCX','MMCM')
+%% -----------------------------------------------------------------
+
+node2 = readmmcnode('node_mesh1.dat');
+elem2 = readmmcelem('elem_mesh1.dat');
+load mesh1.dat;
+mesh1 = reshape(mesh1(:, end), [size(node2, 1), length(mesh1) / size(node2, 1)]);
+s2 = sum(mesh1, 2) * dt;
+[cutpos, cutvalue, facedata] = qmeshcut(elem2(:, 1:4), node2, s2, [0 30 0; 0 30 1; 1 30 0]);
+% patch('Vertices',cutpos,'Faces',facedata,'FaceVertexCData',log10(cutvalue),'FaceColor','interp','linestyle','none');
+% view([0 1 0])
+vi = griddata(cutpos(:, 1), cutpos(:, 3), cutvalue, xi, yi);
+
+figure;
+hold on;
+[cc, hc] = contour(xa + 30, za + 31, log10(abs(phi_ana)), clines, 'color', [0.7 0.7 0.7], 'linewidth', 2);
+contour(log10(squeeze(abs(cwmcx(:, 30, :)))'), clines, 'b-');
+contour(log10(abs(vi)), clines, 'r:');
+plot(xcirc, ycirc, 'k--', 'linewidth', 2);
+
+axis equal;
+set(gca, 'xlim', [1 60]);
+set(gca, 'ylim', [1 60]);
+set(gca, 'fontsize', 18);
+xlabel('x (mm)');
+ylabel('z (mm)');
+legend('Diffusion', 'MCX', 'MMCM');
 legend boxoff;
 box on;
-set(gcf,'PaperPositionMode','auto');
-print -depsc2 mesh1.eps
+set(gcf, 'PaperPositionMode', 'auto');
+print -depsc2 mesh1.eps;
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% plot sphere 3
-%%-----------------------------------------------------------------
-
-node3=readmmcnode('node_mesh2.dat');
-elem3=readmmcelem('elem_mesh2.dat');
-load mesh2.dat
-mesh2=reshape(mesh2(:,end),[size(node3,1),length(mesh2)/size(node3,1)]);
-s3=sum(mesh2,2)*dt;
-[cutpos,cutvalue,facedata]=qmeshcut(elem3(:,1:4),node3,s3,[0 29 0; 0 29 1; 1 29 0]);
-
-vi=griddata(cutpos(:,1),cutpos(:,3),cutvalue,xi,yi);
-
-figure
-%patch('Vertices',cutpos,'Faces',facedata,'FaceVertexCData',log10(cutvalue),'FaceColor','interp','linestyle','none');
-%view([0 1 0])
-hold on
-[cc,hc]=contour(xa+30,za+31,log10(abs(phi_ana)),clines,'color',[0.7 0.7 0.7],'linewidth',2);
-contour(log10(squeeze(abs(cwmcx(:,30,:)))'),clines,'b-')
-contour(log10(abs(vi)),clines,'r:')
-plot(xcirc,ycirc,'k--','linewidth',2);
-
-axis equal
-set(gca,'xlim',[1 60]);
-set(gca,'ylim',[1 60]);
-set(gca,'fontsize',18)
-xlabel('x (mm)')
-ylabel('z (mm)')
-legend('Diffusion','MCX','MMCM')
+%% -----------------------------------------------------------------
+
+node3 = readmmcnode('node_mesh2.dat');
+elem3 = readmmcelem('elem_mesh2.dat');
+load mesh2.dat;
+mesh2 = reshape(mesh2(:, end), [size(node3, 1), length(mesh2) / size(node3, 1)]);
+s3 = sum(mesh2, 2) * dt;
+[cutpos, cutvalue, facedata] = qmeshcut(elem3(:, 1:4), node3, s3, [0 29 0; 0 29 1; 1 29 0]);
+
+vi = griddata(cutpos(:, 1), cutpos(:, 3), cutvalue, xi, yi);
+
+figure;
+% patch('Vertices',cutpos,'Faces',facedata,'FaceVertexCData',log10(cutvalue),'FaceColor','interp','linestyle','none');
+% view([0 1 0])
+hold on;
+[cc, hc] = contour(xa + 30, za + 31, log10(abs(phi_ana)), clines, 'color', [0.7 0.7 0.7], 'linewidth', 2);
+contour(log10(squeeze(abs(cwmcx(:, 30, :)))'), clines, 'b-');
+contour(log10(abs(vi)), clines, 'r:');
+plot(xcirc, ycirc, 'k--', 'linewidth', 2);
+
+axis equal;
+set(gca, 'xlim', [1 60]);
+set(gca, 'ylim', [1 60]);
+set(gca, 'fontsize', 18);
+xlabel('x (mm)');
+ylabel('z (mm)');
+legend('Diffusion', 'MCX', 'MMCM');
 legend boxoff;
 box on;
 
-set(gcf,'PaperPositionMode','auto');
-print -depsc2 mesh2.eps
-
+set(gcf, 'PaperPositionMode', 'auto');
+print -depsc2 mesh2.eps;
diff --git a/examples/misctest/bary_external.m b/examples/misctest/bary_external.m
index 2ab4fb8c..5163f6e5 100644
--- a/examples/misctest/bary_external.m
+++ b/examples/misctest/bary_external.m
@@ -1,18 +1,17 @@
 % test bary centric coordinates outside a tetrahedron
 
-node=[0 0 0;1 0 0;0 1 0;0 0 1];
-elem=[1 2 3 4];
-tetramesh(elem,node);
-view([60,30]);
+node = [0 0 0; 1 0 0; 0 1 0; 0 0 1];
+elem = [1 2 3 4];
+tetramesh(elem, node);
+view([60, 30]);
 hold on;
-b1=[1/3,1/3,1/3,0];
-b2=[0 1/3 1/3 1/3];
-t=-2:0.1:2;
+b1 = [1 / 3, 1 / 3, 1 / 3, 0];
+b2 = [0 1 / 3 1 / 3 1 / 3];
+t = -2:0.1:2;
 
-for i=1:length(t)
- pp=node'*(t(i)*b1+(1-t(i))*b2)';
- plot3(pp(1),pp(2),pp(3),'o');
- axis equal;
- waitforbuttonpress;
+for i = 1:length(t)
+    pp = node' * (t(i) * b1 + (1 - t(i)) * b2)';
+    plot3(pp(1), pp(2), pp(3), 'o');
+    axis equal;
+    waitforbuttonpress;
 end
-
diff --git a/examples/onecube/createmesh.m b/examples/onecube/createmesh.m
index dd29d247..8cc41749 100644
--- a/examples/onecube/createmesh.m
+++ b/examples/onecube/createmesh.m
@@ -1,13 +1,12 @@
-sessionid='onecube';
+sessionid = 'onecube';
 
 addpath('../../matlab/');
-[node,elem]=genT6mesh(0:1,0:1,0:1);
-elem=sortrows(elem);
-elem(:,1:4)=meshreorient(node,elem(:,1:4));
+[node, elem] = genT6mesh(0:1, 0:1, 0:1);
+elem = sortrows(elem);
+elem(:, 1:4) = meshreorient(node, elem(:, 1:4));
 
-node=node*10;
-
-srcpos=[2,8,0];
-savemmcmesh(sessionid,node,elem,[]);
-eid=tsearchn(node,elem(:,1:4),srcpos)
+node = node * 10;
 
+srcpos = [2, 8, 0];
+savemmcmesh(sessionid, node, elem, []);
+eid = tsearchn(node, elem(:, 1:4), srcpos);
diff --git a/examples/onecube/plotmmcdebug.m b/examples/onecube/plotmmcdebug.m
index 456993af..8d5c5bdb 100644
--- a/examples/onecube/plotmmcdebug.m
+++ b/examples/onecube/plotmmcdebug.m
@@ -1,26 +1,26 @@
 addpath('../../matlab/');
-node=readmmcnode('node_onecube.dat');
-elem=readmmcelem('elem_onecube.dat');
+node = readmmcnode('node_onecube.dat');
+elem = readmmcelem('elem_onecube.dat');
 
-load ad.txt
-load mov.txt
-srcpos=[2 8 0];
+load ad.txt;
+load mov.txt;
+srcpos = [2 8 0];
 
-hh=tetramesh(elem(:,1:4),node);
-set(hh,'facealpha',0.1)
-hold on
+hh = tetramesh(elem(:, 1:4), node);
+set(hh, 'facealpha', 0.1);
+hold on;
 
-photonnum=max(mov(:,end-1));
-tracks=[];
-for i=0:photonnum
-     idx=find(mov(:,end-1)==i);
-     tracks=[tracks; [srcpos(1);mov(idx,2)],[srcpos(2);mov(idx,3)],[srcpos(3);mov(idx,4)]; nan nan nan];
+photonnum = max(mov(:, end - 1));
+tracks = [];
+for i = 0:photonnum
+    idx = find(mov(:, end - 1) == i);
+    tracks = [tracks; [srcpos(1); mov(idx, 2)], [srcpos(2); mov(idx, 3)], [srcpos(3); mov(idx, 4)]; nan nan nan];
 end
-plot3(tracks(:,1),tracks(:,2),tracks(:,3),'.-');
-idx=find(mov(:,1)==0);
-plot3(mov(idx,2),mov(idx,3),mov(idx,4),'ko');
+plot3(tracks(:, 1), tracks(:, 2), tracks(:, 3), '.-');
+idx = find(mov(:, 1) == 0);
+plot3(mov(idx, 2), mov(idx, 3), mov(idx, 4), 'ko');
 
-idx=find(mov(:,1)==2);
-plot3(mov(idx,2),mov(idx,3),mov(idx,4),'+');
+idx = find(mov(:, 1) == 2);
+plot3(mov(idx, 2), mov(idx, 3), mov(idx, 4), '+');
 
-plot3(ad(:,1),ad(:,2),ad(:,3),'r.');
+plot3(ad(:, 1), ad(:, 2), ad(:, 3), 'r.');
diff --git a/examples/planar/addsource_digimouse.m b/examples/planar/addsource_digimouse.m
index 5a59159c..ce5ee486 100644
--- a/examples/planar/addsource_digimouse.m
+++ b/examples/planar/addsource_digimouse.m
@@ -1,20 +1,20 @@
-if(~exist('Digimouse_Mesh_1L.mat','file'))
-     if(~exist('digimouse_mesh_version_1L.tar.gz','file'))
-         websave('digimouse_mesh_version_1L.tar.gz','http://downloads.sourceforge.net/project/mcx/mmc/Digimouse%20FEM%20Mesh/Version%201/digimouse_mesh_version_1L.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fmcx%2Ffiles%2Fmmc%2FDigimouse%2520FEM%2520Mesh%2FVersion%25201%2F&ts=1450931781&use_mirror=skylineservers');
-     end
-     if(~exist('digimouse_mesh_version_1L.tar','file'))
-         gunzip('digimouse_mesh_version_1L.tar.gz');
-     end
-     if(~exist('digimouse_mesh/Digimouse_Mesh_1L.mat','file'))
-         untar('digimouse_mesh_version_1L.tar');
-         movefile('digimouse_mesh/Digimouse_Mesh_1L.mat','./Digimouse_Mesh_1L.mat');
-     end
+if (~exist('Digimouse_Mesh_1L.mat', 'file'))
+    if (~exist('digimouse_mesh_version_1L.tar.gz', 'file'))
+        websave('digimouse_mesh_version_1L.tar.gz', 'http://downloads.sourceforge.net/project/mcx/mmc/Digimouse%20FEM%20Mesh/Version%201/digimouse_mesh_version_1L.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fmcx%2Ffiles%2Fmmc%2FDigimouse%2520FEM%2520Mesh%2FVersion%25201%2F&ts=1450931781&use_mirror=skylineservers');
+    end
+    if (~exist('digimouse_mesh_version_1L.tar', 'file'))
+        gunzip('digimouse_mesh_version_1L.tar.gz');
+    end
+    if (~exist('digimouse_mesh/Digimouse_Mesh_1L.mat', 'file'))
+        untar('digimouse_mesh_version_1L.tar');
+        movefile('digimouse_mesh/Digimouse_Mesh_1L.mat', './Digimouse_Mesh_1L.mat');
+    end
 end
 load Digimouse_Mesh_1L;
-elem(:,5)=1;
+elem(:, 5) = 1;
 
-cfg=struct('srctype','planar','srcpos',[15 50 25],'srcdir',[0 0 -1],...
-           'srcparam1',[10 0 0 0],'srcparam2',[0 10 0 0]);
+cfg = struct('srctype', 'planar', 'srcpos', [15 50 25], 'srcdir', [0 0 -1], ...
+             'srcparam1', [10 0 0 0], 'srcparam2', [0 10 0 0]);
 
-[newnode,newelem]=mmcaddsrc(node,elem,cfg);
-savemmcmesh('digimouse',newnode,newelem);
+[newnode, newelem] = mmcaddsrc(node, elem, cfg);
+savemmcmesh('digimouse', newnode, newelem);
diff --git a/examples/planar/plotresult.m b/examples/planar/plotresult.m
index eac35157..98b1fa74 100644
--- a/examples/planar/plotresult.m
+++ b/examples/planar/plotresult.m
@@ -1,8 +1,7 @@
-figure
-load enterpos.txt
+figure;
+load enterpos.txt;
 subplot(121);
-plotmesh(enterpos(:,1:3),'.')
-load exitpos.txt 
+plotmesh(enterpos(:, 1:3), '.');
+load exitpos.txt;
 subplot(122);
-plotmesh(exitpos(:,1:3),'.') 
-
+plotmesh(exitpos(:, 1:3), '.');
diff --git a/examples/reftest/createmesh.m b/examples/reftest/createmesh.m
index 8513a128..6868beed 100644
--- a/examples/reftest/createmesh.m
+++ b/examples/reftest/createmesh.m
@@ -1,15 +1,14 @@
-sessionid='onecube';
+sessionid = 'onecube';
 
 addpath('../../matlab/');
-[node,elem]=genT6mesh(0:1,0:1,0:1);
-elem=sortrows(elem);
-elem(:,1:4)=meshreorient(node,elem(:,1:4));
-elem(:,5)=1;
+[node, elem] = genT6mesh(0:1, 0:1, 0:1);
+elem = sortrows(elem);
+elem(:, 1:4) = meshreorient(node, elem(:, 1:4));
+elem(:, 5) = 1;
 
-node=node*10;
-
-srcpos=[2,8,0];
-eid=tsearchn(node,elem(:,1:4),srcpos)
-elem(eid,5)=2;
-savemmcmesh(sessionid,node,elem,[]);
+node = node * 10;
 
+srcpos = [2, 8, 0];
+eid = tsearchn(node, elem(:, 1:4), srcpos);
+elem(eid, 5) = 2;
+savemmcmesh(sessionid, node, elem, []);
diff --git a/examples/reftest/plotmmcdebug.m b/examples/reftest/plotmmcdebug.m
index f0c2a62b..d03409ab 100644
--- a/examples/reftest/plotmmcdebug.m
+++ b/examples/reftest/plotmmcdebug.m
@@ -1,26 +1,26 @@
 addpath('../../matlab/');
-node=readmmcnode('node_onecube.dat');
-elem=readmmcelem('elem_onecube.dat');
+node = readmmcnode('node_onecube.dat');
+elem = readmmcelem('elem_onecube.dat');
 
-load ad.txt
-load mov.txt
+load ad.txt;
+load mov.txt;
 
 figure;
-hh=tetramesh(elem,node);
-set(hh,'facealpha',0.1)
-hold on
-photonnum=max(mov(:,end-1));
-for i=0:photonnum
-     idx=find(mov(:,end-1)==i);
-     plot3(mov(idx,2),mov(idx,3),mov(idx,4),'.-');
+hh = tetramesh(elem, node);
+set(hh, 'facealpha', 0.1);
+hold on;
+photonnum = max(mov(:, end - 1));
+for i = 0:photonnum
+    idx = find(mov(:, end - 1) == i);
+    plot3(mov(idx, 2), mov(idx, 3), mov(idx, 4), '.-');
 end
-idx=find(mov(:,1)==0);
-plot3(mov(idx,2),mov(idx,3),mov(idx,4),'co');
+idx = find(mov(:, 1) == 0);
+plot3(mov(idx, 2), mov(idx, 3), mov(idx, 4), 'co');
 
-idx=find(mov(:,1)==2);
-plot3(mov(idx,2),mov(idx,3),mov(idx,4),'+');
+idx = find(mov(:, 1) == 2);
+plot3(mov(idx, 2), mov(idx, 3), mov(idx, 4), '+');
 
-idx=find(mov(:,1)==3);
-plot3(mov(idx,2),mov(idx,3),mov(idx,4),'co');
+idx = find(mov(:, 1) == 3);
+plot3(mov(idx, 2), mov(idx, 3), mov(idx, 4), 'co');
 
-plot3(ad(:,1),ad(:,2),ad(:,3),'r.');
+plot3(ad(:, 1), ad(:, 2), ad(:, 3), 'r.');
diff --git a/examples/regression/exitangle/phantom.m b/examples/regression/exitangle/phantom.m
index a37ac0e8..b971be2f 100644
--- a/examples/regression/exitangle/phantom.m
+++ b/examples/regression/exitangle/phantom.m
@@ -1,18 +1,18 @@
 clear;
-phantom_l=50;
-phantom_w=40;
-phantom_h=21;
-bar_dis=16.8;
-bar_h=11;
-bar_c1=[(phantom_l-bar_dis)/2,bar_h];
-bar_c2=[(phantom_l+bar_dis)/2,bar_h];
+phantom_l = 50;
+phantom_w = 40;
+phantom_h = 21;
+bar_dis = 16.8;
+bar_h = 11;
+bar_c1 = [(phantom_l - bar_dis) / 2, bar_h];
+bar_c2 = [(phantom_l + bar_dis) / 2, bar_h];
 
 %% old mesh
 
-[node,face,elem] = meshabox([0 0 0],[phantom_l phantom_w phantom_h],1.2,10); 
-elem(:,1:4) = meshreorient(node(:,1:3),elem(:,1:4));
-elem(:,5) = 1;
-plotmesh(node,elem);
+[node, face, elem] = meshabox([0 0 0], [phantom_l phantom_w phantom_h], 1.2, 10);
+elem(:, 1:4) = meshreorient(node(:, 1:3), elem(:, 1:4));
+elem(:, 5) = 1;
+plotmesh(node, elem);
 
 % savemmcmesh('tank',node,elem);
 
@@ -22,10 +22,10 @@
 source_dir = [0 0 -1];
 param1 = [40 0 0 0];
 param2 = [0 30 0 0];
-cfg=struct('srctype','planar','srcpos',source,'srcdir',source_dir,'srcparam1',param1,'srcparam2',param2);
-source_domain = mmcsrcdomain(cfg,[min(node);max(node)]);
+cfg = struct('srctype', 'planar', 'srcpos', source, 'srcdir', source_dir, 'srcparam1', param1, 'srcparam2', param2);
+source_domain = mmcsrcdomain(cfg, [min(node); max(node)]);
 
-[newnode,newelem] = mmcaddsrc(node,elem,source_domain);
-plotmesh(newnode,newelem);
+[newnode, newelem] = mmcaddsrc(node, elem, source_domain);
+plotmesh(newnode, newelem);
 
-savemmcmesh('tank',newnode,newelem);
+savemmcmesh('tank', newnode, newelem);
diff --git a/examples/regression/exitangle/testexitdir.m b/examples/regression/exitangle/testexitdir.m
index 2317209a..23888900 100644
--- a/examples/regression/exitangle/testexitdir.m
+++ b/examples/regression/exitangle/testexitdir.m
@@ -1,7 +1,6 @@
-dat=loadmch('tank_planar.mch');
-dd=dat(:,7:9);
-dl=sqrt(sum(dd.*dd,2));
+dat = loadmch('tank_planar.mch');
+dd = dat(:, 7:9);
+dl = sqrt(sum(dd .* dd, 2));
 % plot(dl)
 
-find(sum(dd(:,1:2).*dd(:,1:2),2)<1e-5)
-
+find(sum(dd(:, 1:2) .* dd(:, 1:2), 2) < 1e-5);
diff --git a/examples/replay/createmesh.m b/examples/replay/createmesh.m
index b6e5d25b..0c87c426 100644
--- a/examples/replay/createmesh.m
+++ b/examples/replay/createmesh.m
@@ -1,8 +1,7 @@
-
 % you may also use meshgrid5 in iso2mesh 1.7.9 or newer
 % it is identical to genT5mesh
 
-srcpos=[30.1 30.2 0.0];
-[node,elem]=genT6mesh(0:2:60,0:2:60,0:2:60);
-e0=tsearchn(node,elem,srcpos)
-savemmcmesh('replaytest',node,elem);
+srcpos = [30.1 30.2 0.0];
+[node, elem] = genT6mesh(0:2:60, 0:2:60, 0:2:60);
+e0 = tsearchn(node, elem, srcpos);
+savemmcmesh('replaytest', node, elem);
diff --git a/examples/replay/plotjacobian.m b/examples/replay/plotjacobian.m
index e987af1a..5963687f 100644
--- a/examples/replay/plotjacobian.m
+++ b/examples/replay/plotjacobian.m
@@ -1,53 +1,53 @@
 % verify the replay outcome and plot the Jacobian profile
 
 % the photons detected in the original run
-[data1,header1]=loadmch('step1.mch');
-header1
+[data1, header1] = loadmch('step1.mch');
+header1;
 
 % the photons detected in the wl replay phase
-[data2,header2]=loadmch('step2.mch');
-header2
+[data2, header2] = loadmch('step2.mch');
+header2;
 
 % the photons detected in the wp replay phase
-[data3,header3]=loadmch('step3.mch');
-header3
+[data3, header3] = loadmch('step3.mch');
+header3;
 
-data1=data1(data1(:,1)==1,:);
+data1 = data1(data1(:, 1) == 1, :);
 
 % the two sets of captured photons should be identical
-if(all(ismember(round(data1*1e10)*1e-10,round(data2*1e10)*1e-10,'rows')) && ...
-   all(ismember(round(data1*1e10)*1e-10,round(data2*1e10)*1e-10,'rows')))
-   disp('replay is successful :-)');
+if (all(ismember(round(data1 * 1e10) * 1e-10, round(data2 * 1e10) * 1e-10, 'rows')) && ...
+    all(ismember(round(data1 * 1e10) * 1e-10, round(data2 * 1e10) * 1e-10, 'rows')))
+    disp('replay is successful :-)');
 else
-   disp('replay failed :-(');
+    disp('replay failed :-(');
 end
 
 % plot the wl profile
 
-load step2.dat
-[no,el]=readmmcmesh('replaytest');
+load step2.dat;
+[no, el] = readmmcmesh('replaytest');
 
 figure;
-plotmesh([no,log10(step2(:,2))],el(:,1:4),'z=0.2','linestyle','none');
+plotmesh([no, log10(step2(:, 2))], el(:, 1:4), 'z=0.2', 'linestyle', 'none');
 hold on;
-plotmesh([no,log10(step2(:,2))],el(:,1:4),'x=30','linestyle','none');
-view(3)
-set(gca,'xlim',[0 60])
-set(gca,'ylim',[0 60])
-set(gca,'zlim',[0 60])
-shading interp
+plotmesh([no, log10(step2(:, 2))], el(:, 1:4), 'x=30', 'linestyle', 'none');
+view(3);
+set(gca, 'xlim', [0 60]);
+set(gca, 'ylim', [0 60]);
+set(gca, 'zlim', [0 60]);
+shading interp;
 
 % plot the wp profile
 
-load step3.dat
-[no,el]=readmmcmesh('replaytest');
+load step3.dat;
+[no, el] = readmmcmesh('replaytest');
 
 figure;
-plotmesh([no,log10(step3(:,2))],el(:,1:4),'z=0.2','linestyle','none');
+plotmesh([no, log10(step3(:, 2))], el(:, 1:4), 'z=0.2', 'linestyle', 'none');
 hold on;
-plotmesh([no,log10(step3(:,2))],el(:,1:4),'x=30','linestyle','none');
-view(3)
-set(gca,'xlim',[0 60])
-set(gca,'ylim',[0 60])
-set(gca,'zlim',[0 60])
-shading interp
\ No newline at end of file
+plotmesh([no, log10(step3(:, 2))], el(:, 1:4), 'x=30', 'linestyle', 'none');
+view(3);
+set(gca, 'xlim', [0 60]);
+set(gca, 'ylim', [0 60]);
+set(gca, 'zlim', [0 60]);
+shading interp;
diff --git a/examples/replaywide/createmesh.m b/examples/replaywide/createmesh.m
index cfd25784..7f48a06c 100644
--- a/examples/replaywide/createmesh.m
+++ b/examples/replaywide/createmesh.m
@@ -1,30 +1,29 @@
-
 %% original mesh
 
-[node,face,elem]=meshabox([0 0 0],[60 60 20],2, 2);
-elem(:,5)=1;
+[node, face, elem] = meshabox([0 0 0], [60 60 20], 2, 2);
+elem(:, 5) = 1;
 
 figure(1);
-plotmesh(node,elem);
+plotmesh(node, elem);
 
 %% extended source domain
 
-srcdef=struct('srctype','planar','srcpos',[10,10,-2],'srcdir',[0 0 1],...
-                'srcparam1',[40 0 0 40],'srcparam2',[0 40 0 40]);
-            
-[newnode,newelem]=mmcaddsrc(node,elem,srcdef);
+srcdef = struct('srctype', 'planar', 'srcpos', [10, 10, -2], 'srcdir', [0 0 1], ...
+                'srcparam1', [40 0 0 40], 'srcparam2', [0 40 0 40]);
+
+[newnode, newelem] = mmcaddsrc(node, elem, srcdef);
 
 figure(2);
-plotmesh(newnode,newelem);
+plotmesh(newnode, newelem);
 
 %% extended detector domain
 
-detdef=struct('srctype','planar','srcpos',[10,10,20.1],'srcdir',[0 0 -1],...
-                'srcparam1',[40 0 0 40],'srcparam2',[0 40 0 40]);
-            
-[newnode2,newelem2]=mmcadddet(newnode,newelem,detdef);
+detdef = struct('srctype', 'planar', 'srcpos', [10, 10, 20.1], 'srcdir', [0 0 -1], ...
+                'srcparam1', [40 0 0 40], 'srcparam2', [0 40 0 40]);
+
+[newnode2, newelem2] = mmcadddet(newnode, newelem, detdef);
 
 figure(3);
-plotmesh(newnode2,newelem2);
+plotmesh(newnode2, newelem2);
 
-savemmcmesh('replaywide',newnode2,newelem2);
\ No newline at end of file
+savemmcmesh('replaywide', newnode2, newelem2);
diff --git a/examples/replaywide/createpattern.m b/examples/replaywide/createpattern.m
index cdcc37d5..472076d4 100644
--- a/examples/replaywide/createpattern.m
+++ b/examples/replaywide/createpattern.m
@@ -1,23 +1,22 @@
-
 % full field illumination pattern
 pat0 = ones(40);
 
 % pattern with left half dark
 pat1 = pat0;
-pat1(1:20,:) = 0;
+pat1(1:20, :) = 0;
 
 % pattern with top half dark
 pat2 = pat0;
-pat2(:,1:20) = 0;
+pat2(:, 1:20) = 0;
 
-fid=fopen('pattern0.pat','wb','ieee-le');
-fwrite(fid,pat0','float');
+fid = fopen('pattern0.pat', 'wb', 'ieee-le');
+fwrite(fid, pat0', 'float');
 fclose(fid);
 
-fid=fopen('pattern1.pat','wb','ieee-le');
-fwrite(fid,pat1','float');
+fid = fopen('pattern1.pat', 'wb', 'ieee-le');
+fwrite(fid, pat1', 'float');
 fclose(fid);
 
-fid=fopen('pattern2.pat','wb','ieee-le');
-fwrite(fid,pat2','float');
-fclose(fid);
\ No newline at end of file
+fid = fopen('pattern2.pat', 'wb', 'ieee-le');
+fwrite(fid, pat2', 'float');
+fclose(fid);
diff --git a/examples/replaywide/plotresults.m b/examples/replaywide/plotresults.m
index df48e454..b5f2ab8e 100644
--- a/examples/replaywide/plotresults.m
+++ b/examples/replaywide/plotresults.m
@@ -1,15 +1,14 @@
+[node, face, elem] = meshabox([0 0 0], [60 60 20], 2, 2);
 
-[node,face,elem]=meshabox([0 0 0],[60 60 20],2, 2);
-
-data1=load('replay1.dat');
-data2=load('replay2.dat');
-data3=load('replay3.dat');
+data1 = load('replay1.dat');
+data2 = load('replay2.dat');
+data3 = load('replay3.dat');
 
 figure(1);
-plotmesh([node,log(data1(1:end-7,2))],elem);
+plotmesh([node, log(data1(1:end - 7, 2))], elem);
 
 figure(2);
-plotmesh([node,log(data2(1:end-7,2))],elem);
+plotmesh([node, log(data2(1:end - 7, 2))], elem);
 
 figure(3);
-plotmesh([node,log(data3(1:end-7,2))],elem);
\ No newline at end of file
+plotmesh([node, log(data3(1:end - 7, 2))], elem);
diff --git a/examples/sfdi2layer/createmesh.m b/examples/sfdi2layer/createmesh.m
index 5c1ca78e..75da40c5 100644
--- a/examples/sfdi2layer/createmesh.m
+++ b/examples/sfdi2layer/createmesh.m
@@ -2,43 +2,45 @@
 
 %% 2-layer mesh model
 
-layercount=2;
+layercount = 2;
+
+if (layercount == 2)
+    [node, face, c0] = latticegrid([0 60], [0 60], [0 25 30]);
+    c0(:, 4) = [2; 1];   % maximum element size for bottom (label 1) and top (label 2) layers
 
-if(layercount==2)
-    [node,face,c0]=latticegrid([0 60],[0 60],[0 25 30]);
-    c0(:,4)=[2;1];   % maximum element size for bottom (label 1) and top (label 2) layers
-    
     % simulate the optical properties of skull and gray-matter of a human brain model
     % see http://mcx.sourceforge.net/cgi-bin/index.cgi?MMC/Colin27AtlasMesh
-    % cfg.prop=[0 0 1 1;0.02 9.0, 0.89 1.37;0.019 7.8 0.89 1.37]; 
+    % cfg.prop=[0 0 1 1;0.02 9.0, 0.89 1.37;0.019 7.8 0.89 1.37];
 else
-    [node,face,c0]=latticegrid([0 60],[0 60],[0 20 25 30]); % if you like a 3-layer model
-    c0(:,4)=[2;2;1];
-    % cfg.prop=[0 0 1 1;0.02 9.0, 0.89 1.37;0.004 0.009, 0.89 1.37;0.019 7.8 0.89 1.37]; 
+    [node, face, c0] = latticegrid([0 60], [0 60], [0 20 25 30]); % if you like a 3-layer model
+    c0(:, 4) = [2; 2; 1];
+    % cfg.prop=[0 0 1 1;0.02 9.0, 0.89 1.37;0.004 0.009, 0.89 1.37;0.019 7.8 0.89 1.37];
 end
-[no,el]=surf2mesh(node,face,[],[],1,[],c0);
+[no, el] = surf2mesh(node, face, [], [], 1, [], c0);
 
-figure(1); plotmesh(no,el);
-savemmcmesh('media',no,el);
+figure(1);
+plotmesh(no, el);
+savemmcmesh('media', no, el);
 
 %% add source and retessellate mesh
 
-cfg.srctype='fourier';
-cfg.srcpos=[10 10 35];
-kx=3;                       % wave number in the x-dir
-ky=0;                       % wave number in the x-dir
-xphase=pi/3;                % phase offset in the x-dir, must < 2pi
-yphase=0;                   % phase offset in the x-dir, must < 2pi
-cfg.srcparam1=[40 0 0 kx+xphase/(2*pi)];   % 3 is k-number in x direction
-cfg.srcparam2=[0 40 0 ky+yphase/(2*pi)];
-cfg.srcdir=[0 0 -1];
+cfg.srctype = 'fourier';
+cfg.srcpos = [10 10 35];
+kx = 3;                       % wave number in the x-dir
+ky = 0;                       % wave number in the x-dir
+xphase = pi / 3;                % phase offset in the x-dir, must < 2pi
+yphase = 0;                   % phase offset in the x-dir, must < 2pi
+cfg.srcparam1 = [40 0 0 kx + xphase / (2 * pi)];   % 3 is k-number in x direction
+cfg.srcparam2 = [0 40 0 ky + yphase / (2 * pi)];
+cfg.srcdir = [0 0 -1];
 
-srcdef=struct('srctype',cfg.srctype,'srcpos',cfg.srcpos,'srcdir',cfg.srcdir,...
-    'srcparam1',cfg.srcparam1,'srcparam2',cfg.srcparam2);
+srcdef = struct('srctype', cfg.srctype, 'srcpos', cfg.srcpos, 'srcdir', cfg.srcdir, ...
+                'srcparam1', cfg.srcparam1, 'srcparam2', cfg.srcparam2);
 
-[node,elem] = mmcaddsrc(no,el,mmcsrcdomain(srcdef,[min(no);max(no)]));
+[node, elem] = mmcaddsrc(no, el, mmcsrcdomain(srcdef, [min(no); max(no)]));
 
-figure(2); plotmesh(node,elem);
+figure(2);
+plotmesh(node, elem);
 
 % save the final re-tessellated mesh
-savemmcmesh('sfdi',node,elem);
+savemmcmesh('sfdi', node, elem);
diff --git a/examples/sfdi2layer/plot_result.m b/examples/sfdi2layer/plot_result.m
index a6d06bcb..7651d47c 100644
--- a/examples/sfdi2layer/plot_result.m
+++ b/examples/sfdi2layer/plot_result.m
@@ -1,17 +1,18 @@
 % CW fluence
 data = load('sfdi.dat');
-data = reshape(data(:,2),[],50);
-layercw = sum(data(1:end-3,:),2)*1e-10;
+data = reshape(data(:, 2), [], 50);
+layercw = sum(data(1:end - 3, :), 2) * 1e-10;
 
 % media mesh
 cfg.node = readmmcnode('node_media.dat');
 cfg.elem = readmmcelem('elem_media.dat');
-cfg.elemprop=cfg.elem(:,5);
+cfg.elemprop = cfg.elem(:, 5);
 
 % plot results
 hold on;
-qmeshcut(cfg.elem(cfg.elemprop>0,1:4),cfg.node,log10(layercw),'y=30','linestyle','none'); view(3)
-qmeshcut(cfg.elem(cfg.elemprop>0,1:4),cfg.node,log10(layercw),'z=27','linestyle','none');
+qmeshcut(cfg.elem(cfg.elemprop > 0, 1:4), cfg.node, log10(layercw), 'y=30', 'linestyle', 'none');
+view(3);
+qmeshcut(cfg.elem(cfg.elemprop > 0, 1:4), cfg.node, log10(layercw), 'z=27', 'linestyle', 'none');
 box on;
-axis equal
+axis equal;
 view(-56, 22);
diff --git a/examples/sharing/createmesh.m b/examples/sharing/createmesh.m
index 61678183..2fc68824 100644
--- a/examples/sharing/createmesh.m
+++ b/examples/sharing/createmesh.m
@@ -1,20 +1,19 @@
-
 %% original mesh
 
-[node,face,elem]=meshabox([0 0 0],[60 60 20],2, 2);
-elem(:,5)=1;
+[node, face, elem] = meshabox([0 0 0], [60 60 20], 2, 2);
+elem(:, 5) = 1;
 
 figure(1);
-plotmesh(node,elem);
+plotmesh(node, elem);
 
 %% extended source domain
 
-srcdef=struct('srctype','planar','srcpos',[10,10,-2],'srcdir',[0 0 1],...
-                'srcparam1',[40 0 0 40],'srcparam2',[0 40 0 40]);
-            
-[newnode,newelem]=mmcaddsrc(node,elem,srcdef);
+srcdef = struct('srctype', 'planar', 'srcpos', [10, 10, -2], 'srcdir', [0 0 1], ...
+                'srcparam1', [40 0 0 40], 'srcparam2', [0 40 0 40]);
+
+[newnode, newelem] = mmcaddsrc(node, elem, srcdef);
 
 figure(2);
-plotmesh(newnode,newelem);
+plotmesh(newnode, newelem);
 
-savemmcmesh('sharing',newnode,newelem);
\ No newline at end of file
+savemmcmesh('sharing', newnode, newelem);
diff --git a/examples/sharing/createpattern.m b/examples/sharing/createpattern.m
index 1bc3d599..32215e2b 100644
--- a/examples/sharing/createpattern.m
+++ b/examples/sharing/createpattern.m
@@ -1,28 +1,27 @@
-
 % full field illumination pattern
 pat0 = ones(40);
 
 % pattern with left half bright
 pat1 = zeros(40);
-pat1(1:20,:) = 1;
+pat1(1:20, :) = 1;
 
 % pattern with top half bright
 pat2 = zeros(40);
-pat2(:,1:20) = 1;
+pat2(:, 1:20) = 1;
 
 % pattern with bright square in the middle
 pat3 = zeros(40);
-pat3(11:30,11:30) = 1;
+pat3(11:30, 11:30) = 1;
 
 % pattern with a bright cross
 pat4 = zeros(40);
-pat4(16:25,:) = 1;
-pat4(:,16:25) = 1;
+pat4(16:25, :) = 1;
+pat4(:, 16:25) = 1;
 
-fid=fopen('patterns.pat','wb','ieee-le');
-fwrite(fid,pat0','float');
-fwrite(fid,pat1','float');
-fwrite(fid,pat2','float');
-fwrite(fid,pat3','float');
-fwrite(fid,pat4','float');
-fclose(fid);
\ No newline at end of file
+fid = fopen('patterns.pat', 'wb', 'ieee-le');
+fwrite(fid, pat0', 'float');
+fwrite(fid, pat1', 'float');
+fwrite(fid, pat2', 'float');
+fwrite(fid, pat3', 'float');
+fwrite(fid, pat4', 'float');
+fclose(fid);
diff --git a/examples/sharing/plotresults.m b/examples/sharing/plotresults.m
index 8c1f19a5..c460f68d 100644
--- a/examples/sharing/plotresults.m
+++ b/examples/sharing/plotresults.m
@@ -1,43 +1,47 @@
-
 % [node,face,elem]=meshabox([0 0 0],[60 60 20],2, 2);
 nTG = 50;
 npat = 5;
 
-rawdata=load('sharing.dat');
-data=reshape(rawdata(:,end),npat,[],nTG);
-cwdata=squeeze(sum(data,3));
-cwdata=cwdata(:,1:end-3);
+rawdata = load('sharing.dat');
+data = reshape(rawdata(:, end), npat, [], nTG);
+cwdata = squeeze(sum(data, 3));
+cwdata = cwdata(:, 1:end - 3);
 
 %% plot results
 
 figure();
 
-subplot(1,3,1); title('pattern 1');
-plotmesh([node,(cwdata(1,:))'],elem,'linestyle','none');
-shading interp
-axis off
-view([0,0,-1])
-
-subplot(2,3,2); title('pattern 2');
-plotmesh([node,(cwdata(2,:))'],elem,'linestyle','none');
-shading interp
-axis off
-view([0,0,-1])
-
-subplot(2,3,3); title('pattern 3');
-plotmesh([node,(cwdata(3,:))'],elem,'linestyle','none');
-shading interp
-axis off
-view([0,0,-1])
-
-subplot(2,3,5); title('pattern 4');
-plotmesh([node,(cwdata(4,:))'],elem,'linestyle','none');
-shading interp
-axis off
-view([0,0,-1])
-
-subplot(2,3,6); title('pattern 5');
-plotmesh([node,(cwdata(5,:))'],elem,'linestyle','none');
-shading interp
-axis off
-view([0,0,-1])
\ No newline at end of file
+subplot(1, 3, 1);
+title('pattern 1');
+plotmesh([node, (cwdata(1, :))'], elem, 'linestyle', 'none');
+shading interp;
+axis off;
+view([0, 0, -1]);
+
+subplot(2, 3, 2);
+title('pattern 2');
+plotmesh([node, (cwdata(2, :))'], elem, 'linestyle', 'none');
+shading interp;
+axis off;
+view([0, 0, -1]);
+
+subplot(2, 3, 3);
+title('pattern 3');
+plotmesh([node, (cwdata(3, :))'], elem, 'linestyle', 'none');
+shading interp;
+axis off;
+view([0, 0, -1]);
+
+subplot(2, 3, 5);
+title('pattern 4');
+plotmesh([node, (cwdata(4, :))'], elem, 'linestyle', 'none');
+shading interp;
+axis off;
+view([0, 0, -1]);
+
+subplot(2, 3, 6);
+title('pattern 5');
+plotmesh([node, (cwdata(5, :))'], elem, 'linestyle', 'none');
+shading interp;
+axis off;
+view([0, 0, -1]);
diff --git a/examples/skinvessel/createsession.m b/examples/skinvessel/createsession.m
index 02a5c1e5..dcb0cd0b 100644
--- a/examples/skinvessel/createsession.m
+++ b/examples/skinvessel/createsession.m
@@ -1,80 +1,78 @@
 %% create the skin-vessel benchmark mesh
-[no,fc]=latticegrid([0 200],[0 200],[20 32 200]); % create a 3-layer tissue
-no(end,:)=no(end,:)+1e-5;
+[no, fc] = latticegrid([0 200], [0 200], [20 32 200]); % create a 3-layer tissue
+no(end, :) = no(end, :) + 1e-5;
 
-fc2=cell2mat(fc);
-fc=[fc2(:,[1 2 3]); fc2(:,[1 3 4])];
+fc2 = cell2mat(fc);
+fc = [fc2(:, [1 2 3]); fc2(:, [1 3 4])];
 
-[ncy,fcy]=meshacylinder([-1,99.5,99.5],[201,99.5,99.5],20,5); % add the vessel
-[newnode,newelem]=surfboolean(no,fc,'first',ncy,fcy);  % merge the two domains
+[ncy, fcy] = meshacylinder([-1, 99.5, 99.5], [201, 99.5, 99.5], 20, 5); % add the vessel
+[newnode, newelem] = surfboolean(no, fc, 'first', ncy, fcy);  % merge the two domains
 
-c0=[10,100,150,26]';
-seeds=[ones(4,2)*100, c0];  % define the regions by index
+c0 = [10, 100, 150, 26]';
+seeds = [ones(4, 2) * 100, c0];  % define the regions by index
 
-[cfg.node,cfg.elem]=s2m(newnode,newelem(:,1:3),1,30,'tetgen',seeds,[],'-YY -A'); % creating the merged mesh domain
+[cfg.node, cfg.elem] = s2m(newnode, newelem(:, 1:3), 1, 30, 'tetgen', seeds, [], '-YY -A'); % creating the merged mesh domain
 
-voxellen=0.005;
-cfg.node=cfg.node*voxellen;
-cfg.method='g';
+voxellen = 0.005;
+cfg.node = cfg.node * voxellen;
+cfg.method = 'g';
 
-figure; 
+figure;
 subplot(121);
-plotmesh(cfg.node,cfg.elem);
+plotmesh(cfg.node, cfg.elem);
 
-cfg.elemprop=cfg.elem(:,5);
-cfg.elem=cfg.elem(:,1:4);
+cfg.elemprop = cfg.elem(:, 5);
+cfg.elem = cfg.elem(:, 1:4);
 
 %% define other properties
 
-cfg.prop=[0.0000         0.0    1.0000    1
-    3.5640e-05    1.0000    1.0000    1.3700
-   23.0543    9.3985    0.9000    1.3700
-    0.0458   35.6541    0.9000    1.3700
-    1.6572   37.5940    0.9000    1.3700];
+cfg.prop = [0.0000         0.0    1.0000    1
+            3.5640e-05    1.0000    1.0000    1.3700
+            23.0543    9.3985    0.9000    1.3700
+            0.0458   35.6541    0.9000    1.3700
+            1.6572   37.5940    0.9000    1.3700];
 
-cfg.srcpos=[100 100 -1]*voxellen;
-cfg.srcdir=[0 0 1];
+cfg.srcpos = [100 100 -1] * voxellen;
+cfg.srcdir = [0 0 1];
 
-cfg.tstart=0;
-cfg.tend=5e-8;
-cfg.tstep=5e-8;
+cfg.tstart = 0;
+cfg.tend = 5e-8;
+cfg.tstep = 5e-8;
 % cfg.outputtype='energy'; %energy deposition in mmc varys with elem volume
-cfg.outputtype='flux';
-cfg.minenergy=0.01;
+cfg.outputtype = 'flux';
+cfg.minenergy = 0.01;
 
-cfg.srctype='disk';
-cfg.srcparam1=[0.3 0 0 0];
+cfg.srctype = 'disk';
+cfg.srcparam1 = [0.3 0 0 0];
 
 %% define wide-field disk source by extending the mesh to the widefield src
-srcdef=struct('srctype',cfg.srctype,'srcpos',cfg.srcpos,'srcdir',cfg.srcdir,...
-    'srcparam1',cfg.srcparam1,'srcparam2',[]);
+srcdef = struct('srctype', cfg.srctype, 'srcpos', cfg.srcpos, 'srcdir', cfg.srcdir, ...
+                'srcparam1', cfg.srcparam1, 'srcparam2', []);
 
-[cfg.node,cfg.elem] = mmcaddsrc(cfg.node,[cfg.elem cfg.elemprop],...
-    mmcsrcdomain(srcdef,[min(cfg.node);max(cfg.node)]));
+[cfg.node, cfg.elem] = mmcaddsrc(cfg.node, [cfg.elem cfg.elemprop], ...
+                                 mmcsrcdomain(srcdef, [min(cfg.node); max(cfg.node)]));
 
-
-cfg.elemprop=cfg.elem(:,5);
-cfg.elem=cfg.elem(:,1:4);
+cfg.elemprop = cfg.elem(:, 5);
+cfg.elem = cfg.elem(:, 1:4);
 
 %% other simulation information
 
-cfg.nphoton=1e7;
-cfg.seed=1648335518;
+cfg.nphoton = 1e7;
+cfg.seed = 1648335518;
 
-cfg.debuglevel='TP';
-cfg.isreflect=0;
+cfg.debuglevel = 'TP';
+cfg.isreflect = 0;
 
 %% saving coarse mesh
-mmc2json(cfg,'dmmc_skinvessel.json');
+mmc2json(cfg, 'dmmc_skinvessel.json');
 
 %% regenerate the mesh using fine mesh
-[cfg.node,cfg.elem]=s2m(newnode,newelem(:,1:3),1,30,'tetgen',seeds,[]); % creating the merged mesh domain
-cfg.node=cfg.node*voxellen;
-cfg.elemprop=cfg.elem(:,5);
-cfg.elem=cfg.elem(:,1:4);
-
-[cfg.node,cfg.elem] = mmcaddsrc(cfg.node,[cfg.elem cfg.elemprop],...
-    mmcsrcdomain(srcdef,[min(cfg.node);max(cfg.node)]));
+[cfg.node, cfg.elem] = s2m(newnode, newelem(:, 1:3), 1, 30, 'tetgen', seeds, []); % creating the merged mesh domain
+cfg.node = cfg.node * voxellen;
+cfg.elemprop = cfg.elem(:, 5);
+cfg.elem = cfg.elem(:, 1:4);
 
-mmc2json(cfg,'skinvessel.json');
+[cfg.node, cfg.elem] = mmcaddsrc(cfg.node, [cfg.elem cfg.elemprop], ...
+                                 mmcsrcdomain(srcdef, [min(cfg.node); max(cfg.node)]));
 
+mmc2json(cfg, 'skinvessel.json');
diff --git a/examples/sphere/addsource_sphere.m b/examples/sphere/addsource_sphere.m
index 267563c1..1b012e6c 100644
--- a/examples/sphere/addsource_sphere.m
+++ b/examples/sphere/addsource_sphere.m
@@ -1,13 +1,13 @@
-[node,face,elem]=meshasphere([0 0 0],24,1,2);
-elem(:,5)=1;
+[node, face, elem] = meshasphere([0 0 0], 24, 1, 2);
+elem(:, 5) = 1;
 
-cfg=struct('srctype','planar','srcpos',[-5 -5 25],'srcdir',[0 0 -1],...
-           'srcparam1',[10 0 0 0],'srcparam2',[0 10 0 0]);
-[newnode,newelem]=mmcaddsrc(node,elem,cfg);
+cfg = struct('srctype', 'planar', 'srcpos', [-5 -5 25], 'srcdir', [0 0 -1], ...
+             'srcparam1', [10 0 0 0], 'srcparam2', [0 10 0 0]);
+[newnode, newelem] = mmcaddsrc(node, elem, cfg);
 
-cfg=struct('srctype','planar','srcpos',[-30 -5 -5],'srcdir',[1 0 0],...
-           'srcparam1',[0 10 0 0],'srcparam2',[0 0 10 0]);
-[nodedet,elemdet]=mmcadddet(newnode,newelem,cfg);
-plotmesh(nodedet,elemdet);
+cfg = struct('srctype', 'planar', 'srcpos', [-30 -5 -5], 'srcdir', [1 0 0], ...
+             'srcparam1', [0 10 0 0], 'srcparam2', [0 0 10 0]);
+[nodedet, elemdet] = mmcadddet(newnode, newelem, cfg);
+plotmesh(nodedet, elemdet);
 
-savemmcmesh('sphere',nodedet,elemdet);
+savemmcmesh('sphere', nodedet, elemdet);
diff --git a/examples/sphere/plotresults.m b/examples/sphere/plotresults.m
index 08ad85b9..426b02b8 100644
--- a/examples/sphere/plotresults.m
+++ b/examples/sphere/plotresults.m
@@ -1,13 +1,12 @@
-no=readmmcnode('node_sphere.dat');
-el=readmmcelem('elem_sphere.dat');
+no = readmmcnode('node_sphere.dat');
+el = readmmcelem('elem_sphere.dat');
 load planar.dat;
-vv=reshape(planar(:,2),size(no,1),size(planar,1)/size(no,1));
-vvv=sum(vv,2);
-plotmesh([no,vvv],el(el(:,end)>0,1:4))
-ppl=loadmch('planar.mch');
-hold on
-plotmesh(ppl(:,4:6),'r.'); % plot detected photon locations from a widefield detector
-figure
-plotmesh([no,log10(vvv)],el(el(:,end)>0,1:4),'x=0');
-shading interp
-
+vv = reshape(planar(:, 2), size(no, 1), size(planar, 1) / size(no, 1));
+vvv = sum(vv, 2);
+plotmesh([no, vvv], el(el(:, end) > 0, 1:4));
+ppl = loadmch('planar.mch');
+hold on;
+plotmesh(ppl(:, 4:6), 'r.'); % plot detected photon locations from a widefield detector
+figure;
+plotmesh([no, log10(vvv)], el(el(:, end) > 0, 1:4), 'x=0');
+shading interp;
diff --git a/examples/sphshells/createsession.m b/examples/sphshells/createsession.m
index a5df92f5..b32435e2 100644
--- a/examples/sphshells/createsession.m
+++ b/examples/sphshells/createsession.m
@@ -1,83 +1,83 @@
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% validate DMMC with MMC in a heterogeneous cubic domain
 %  (see DMMC paper Fig. 1)
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %
-% In this example, we validate the DMMC algorithm with MMC using a 
+% In this example, we validate the DMMC algorithm with MMC using a
 % heterogeneous cubic domain. We also compare the DMMC/MMC solution with
 % that of voxel-based MC (MCX). This simulation generates the results
 % shown in Fig. 1(c-e) in the paper.
-% 
-%%-----------------------------------------------------------------
+%
+%% -----------------------------------------------------------------
 
 % preparation
 
-% 1. you need to add the path to iso2mesh toolbox 
+% 1. you need to add the path to iso2mesh toolbox
 % addpath('/path/to/iso2mesh/toolbox/');
 
 % 2. you need to add the path to MMC matlab folder
 % addpath('../../matlab');
 
 % create a surface mesh for a 10 mm radius sphere
-[nsph_10,fsph_10]=meshasphere([30 30 30],10,1.0);
-[nsph_10,fsph_10]=removeisolatednode(nsph_10,fsph_10);
+[nsph_10, fsph_10] = meshasphere([30 30 30], 10, 1.0);
+[nsph_10, fsph_10] = removeisolatednode(nsph_10, fsph_10);
 
 % create a surface mesh for a 23 mm radius sphere
-[nsph_23,fsph_23]=meshasphere([30 30 30],23,2.0);
-[nsph_23,fsph_23]=removeisolatednode(nsph_23,fsph_23);
+[nsph_23, fsph_23] = meshasphere([30 30 30], 23, 2.0);
+[nsph_23, fsph_23] = removeisolatednode(nsph_23, fsph_23);
 
 % create a surface mesh for a 25 mm radius sphere
-[nsph_25,fsph_25]=meshasphere([30 30 30],25,2.0);
-[nsph_25,fsph_25]=removeisolatednode(nsph_25,fsph_25);
+[nsph_25, fsph_25] = meshasphere([30 30 30], 25, 2.0);
+[nsph_25, fsph_25] = removeisolatednode(nsph_25, fsph_25);
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% create simulation parameters
-%%-----------------------------------------------------------------
-clear cfg
-
-cfg.nphoton=3e6;
-cfg.seed=1648335518;
-cfg.srcpos=[30,30.1,0];
-cfg.srcdir=[0 0 1];
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=5e-10;
-cfg.prop=[0,0,1,1;0.02 7.0 0.89 1.37;0.004 0.009 0.89 1.37;0.02 9.0 0.89 1.37;0.05 0.0 1.0 1.37];
-cfg.debuglevel='TP';
-cfg.isreflect=1;
-
-cfgs=[cfg cfg];
-
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
+clear cfg;
+
+cfg.nphoton = 3e6;
+cfg.seed = 1648335518;
+cfg.srcpos = [30, 30.1, 0];
+cfg.srcdir = [0 0 1];
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 5e-10;
+cfg.prop = [0, 0, 1, 1; 0.02 7.0 0.89 1.37; 0.004 0.009 0.89 1.37; 0.02 9.0 0.89 1.37; 0.05 0.0 1.0 1.37];
+cfg.debuglevel = 'TP';
+cfg.isreflect = 1;
+
+cfgs = [cfg cfg];
+
+%% -----------------------------------------------------------------
 %% tetrahedral mesh generation
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-% generate a coarse CDT volumetric mesh from triangular surfaces of 
+% generate a coarse CDT volumetric mesh from triangular surfaces of
 % three spheres with an additional bounding box for DMMC
 
-ISO2MESH_SESSION='dmmc1_';
+ISO2MESH_SESSION = 'dmmc1_';
 
-[nbox,ebox]=meshgrid6(0:60:60,0:60:60,0:60:60);
-fbox=volface(ebox);
-[no,fc]=mergemesh(nsph_10,fsph_10,nsph_23,fsph_23,nsph_25,fsph_25,nbox,fbox);
-[no,fc]=removeisolatednode(no,fc);
+[nbox, ebox] = meshgrid6(0:60:60, 0:60:60, 0:60:60);
+fbox = volface(ebox);
+[no, fc] = mergemesh(nsph_10, fsph_10, nsph_23, fsph_23, nsph_25, fsph_25, nbox, fbox);
+[no, fc] = removeisolatednode(no, fc);
 
-ISO2MESH_TETGENOPT='-A -q -Y'
-[cfgs(1).node,cfgs(1).elem]=surf2mesh(no,fc,[0 0 0],[60.1 60.1 60.1],1,100,[1 1 1;30 30 6;30 30 15;30 30 30]);%thin layer
+ISO2MESH_TETGENOPT = '-A -q -Y';
+[cfgs(1).node, cfgs(1).elem] = surf2mesh(no, fc, [0 0 0], [60.1 60.1 60.1], 1, 100, [1 1 1; 30 30 6; 30 30 15; 30 30 30]); % thin layer
 % [cfgs(1).node,cfgs(1).elem]=surf2mesh(no,fc,[0 0 0],[60.1 60.1 60.1],1,100,[1 1 1;30 30 6;30 30 17;30 30 30]);%thick layer
-cfgs(1).method='g';
+cfgs(1).method = 'g';
 
-% generate a refined volumetric mesh from triangular surfaces of 
+% generate a refined volumetric mesh from triangular surfaces of
 % three spheres with an additional bounding box for MMC
-clear ISO2MESH_TETGENOPT
-ISO2MESH_SESSION='dmmc2_';
-
-[no,fc]=mergemesh(nsph_10,fsph_10,nsph_23,fsph_23,nsph_25,fsph_25);
-[no,fc]=removeisolatednode(no,fc);
-srcpos=cfgs(1).srcpos;
-[cfgs(2).node,cfgs(2).elem,face2]=surf2mesh(no,fc,[0 0 0],[60 60 60],1,0.25,[1 1 1 0.1;30 30 6 0.1;30 30 17 0.1;30 30 30 0.1],[],[1 1 1 1 1 1 1 1]);
-[cfgs(2).node,cfgs(2).elem]=sortmesh(srcpos,cfgs(2).node,cfgs(2).elem,1:4);
-cfgs(2).method='s';
-
-mmc2json(cfgs(1),'dmmc_sphshells.json');
-mmc2json(cfgs(2),'sphshells.json');
+clear ISO2MESH_TETGENOPT;
+ISO2MESH_SESSION = 'dmmc2_';
+
+[no, fc] = mergemesh(nsph_10, fsph_10, nsph_23, fsph_23, nsph_25, fsph_25);
+[no, fc] = removeisolatednode(no, fc);
+srcpos = cfgs(1).srcpos;
+[cfgs(2).node, cfgs(2).elem, face2] = surf2mesh(no, fc, [0 0 0], [60 60 60], 1, 0.25, [1 1 1 0.1; 30 30 6 0.1; 30 30 17 0.1; 30 30 30 0.1], [], [1 1 1 1 1 1 1 1]);
+[cfgs(2).node, cfgs(2).elem] = sortmesh(srcpos, cfgs(2).node, cfgs(2).elem, 1:4);
+cfgs(2).method = 's';
+
+mmc2json(cfgs(1), 'dmmc_sphshells.json');
+mmc2json(cfgs(2), 'sphshells.json');
diff --git a/examples/statnoise/createmesh.m b/examples/statnoise/createmesh.m
index 5f1526e6..71c3de80 100644
--- a/examples/statnoise/createmesh.m
+++ b/examples/statnoise/createmesh.m
@@ -1,11 +1,10 @@
-sessionid='cube20';
+sessionid = 'cube20';
 
 addpath('../../matlab/');
-[node,elem]=genT5mesh(0:1:20,0:1:20,0:1:20);
+[node, elem] = genT5mesh(0:1:20, 0:1:20, 0:1:20);
 
-elem(:,1:4)=meshreorient(node,elem(:,1:4));
-
-srcpos=[10.1,10.2,0];
-savemmcmesh(sessionid,node,elem,[]);
-eid=tsearchn(node,elem(:,1:4),srcpos)
+elem(:, 1:4) = meshreorient(node, elem(:, 1:4));
 
+srcpos = [10.1, 10.2, 0];
+savemmcmesh(sessionid, node, elem, []);
+eid = tsearchn(node, elem(:, 1:4), srcpos);
diff --git a/examples/statnoise/plotstdhist.m b/examples/statnoise/plotstdhist.m
deleted file mode 100644
index e6d2c0c0..00000000
--- a/examples/statnoise/plotstdhist.m
+++ /dev/null
@@ -1,27 +0,0 @@
-addpath('../../matlab/')
-chpt=[1e4 1e5 1e6 1e7];
-no=readmmcnode('node_cube20.dat');
-
-data=zeros(length(chpt),10,size(no,1));
-for i=1:length(chpt)
-      for j=1:10 
-          dd=load(sprintf('v_%d_%d.dat',j,chpt(i)));
-          data(i,j,:)=dd(:,end);
-      end
-end
-
-%data=log10(data);
-chpt=sqrt(chpt);
-
-figure; hold on;
-sty={'bo-','ro-','ko-','co-','bo:','ro:'};
-pos=[10 10 0;10 10 5;10 10 10;10 10 15;10 5 5;10 5 10];
-
-% plot trial numbers with Coefficient of Variation (100*std/mean)
-
-for i=1:size(pos,1)
-	idx=find(ismember(no,pos(i,:),'rows'));
-	plot(chpt,100*[std(data(1,:,idx)),std(data(2,:,idx)),std(data(3,:,idx)),std(data(4,:,idx))]./chpt ... % standard error
-                    ./[mean(data(1,:,idx)),mean(data(2,:,idx)),mean(data(3,:,idx)),mean(data(4,:,idx))],sty{i});
-end
-hold off;
diff --git a/examples/validation/createmesh.m b/examples/validation/createmesh.m
index 5031ee9e..44c7b600 100644
--- a/examples/validation/createmesh.m
+++ b/examples/validation/createmesh.m
@@ -1,11 +1,10 @@
-sessionid='cube';
+sessionid = 'cube';
 
 addpath('../../matlab/');
-[node,elem]=genT5mesh(0:2:60,0:2:60,0:2:60);
+[node, elem] = genT5mesh(0:2:60, 0:2:60, 0:2:60);
 
-elem(:,1:4)=meshreorient(node,elem(:,1:4));
-
-srcpos=[30.1,30.2,0];
-savemmcmesh(sessionid,node,elem,[]);
-eid=tsearchn(node,elem(:,1:4),srcpos)
+elem(:, 1:4) = meshreorient(node, elem(:, 1:4));
 
+srcpos = [30.1, 30.2, 0];
+savemmcmesh(sessionid, node, elem, []);
+eid = tsearchn(node, elem(:, 1:4), srcpos);
diff --git a/examples/validation/plotcuberes.m b/examples/validation/plotcuberes.m
index 307efa48..b98e940f 100644
--- a/examples/validation/plotcuberes.m
+++ b/examples/validation/plotcuberes.m
@@ -1,82 +1,80 @@
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% add paths to the necessary toolboxes
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-%addpath('/Please/add/path/to/mcx/utils/')
-addpath('../../matlab')
+% addpath('/Please/add/path/to/mcx/utils/')
+addpath('../../matlab');
 
-c0=299792458000;
-t0=0;
-dt=1e-10;
-t1=5e-9;
+c0 = 299792458000;
+t0 = 0;
+dt = 1e-10;
+t1 = 5e-9;
 
-twin=[t0+dt/2:dt:t1];
-gates=length(twin);
+twin = [t0 + dt / 2:dt:t1];
+gates = length(twin);
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% load MCX results
-%%-----------------------------------------------------------------
-mcx=loadmc2('../mcxsph/box.mc2', [60 60 60 gates]);
-cwmcx=sum(mcx,4); 
+%% -----------------------------------------------------------------
+mcx = loadmc2('../mcxsph/box.mc2', [60 60 60 gates]);
+cwmcx = sum(mcx, 4);
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% load MMC results
-%%-----------------------------------------------------------------
-node=readmmcnode('node_cube.dat');
-elem=readmmcelem('elem_cube.dat');
+%% -----------------------------------------------------------------
+node = readmmcnode('node_cube.dat');
+elem = readmmcelem('elem_cube.dat');
 
-load cube.dat
-cube=reshape(cube(:,end),[size(node,1),length(cube)/size(node,1)]);
-cwcb=sum(cube,2);
-[cutpos,cutvalue,facedata]=qmeshcut(elem(:,1:4),node,cwcb,[0 30.2 0; 0 30.2 1; 1 30.2 0]);
+load cube.dat;
+cube = reshape(cube(:, end), [size(node, 1), length(cube) / size(node, 1)]);
+cwcb = sum(cube, 2);
+[cutpos, cutvalue, facedata] = qmeshcut(elem(:, 1:4), node, cwcb, [0 30.2 0; 0 30.2 1; 1 30.2 0]);
 
-[xi,yi]=meshgrid(0.5:60,0:60);
-vi=griddata(cutpos(:,1),cutpos(:,3),cutvalue,xi,yi);
+[xi, yi] = meshgrid(0.5:60, 0:60);
+vi = griddata(cutpos(:, 1), cutpos(:, 3), cutvalue, xi, yi);
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% plot the time-domain TPSF at [30 14 10]
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-figure
+figure;
 
-srcpos=[30 30 0];
-detpos=[30 14 10];
+srcpos = [30 30 0];
+detpos = [30 14 10];
 
-hold on
-semilogy((1:gates)/10,tddiffusion(0.005, 1, c0, 0, srcpos, detpos,twin),'r');
-semilogy((1:gates)/10,squeeze(mcx(detpos(1),detpos(2),detpos(3),:)),'o');
-semilogy((1:gates)/10,squeeze(cube(find(node(:,1)==detpos(1) & node(:,2)==detpos(2) & node(:,3)==detpos(3)),:)),'+');
+hold on;
+semilogy((1:gates) / 10, tddiffusion(0.005, 1, c0, 0, srcpos, detpos, twin), 'r');
+semilogy((1:gates) / 10, squeeze(mcx(detpos(1), detpos(2), detpos(3), :)), 'o');
+semilogy((1:gates) / 10, squeeze(cube(find(node(:, 1) == detpos(1) & node(:, 2) == detpos(2) & node(:, 3) == detpos(3)), :)), '+');
 
-set(gca,'fontsize',20)
-xlabel('t (ns)')
-ylabel('Fluence TPSF (1/mm^2)')
-set(gca,'yscale','log')
-legend('Diffusion','MCX','MMCM')
+set(gca, 'fontsize', 20);
+xlabel('t (ns)');
+ylabel('Fluence TPSF (1/mm^2)');
+set(gca, 'yscale', 'log');
+legend('Diffusion', 'MCX', 'MMCM');
 legend boxoff;
 box on;
 
-set(gcf,'PaperPositionMode','auto');
-saveas(gcf,'box_td.fig');
+set(gcf, 'PaperPositionMode', 'auto');
+saveas(gcf, 'box_td.fig');
 
-
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% generate a contour plot along y=30.2
-%%-----------------------------------------------------------------
-figure
-
-hold on
-contour(log10(squeeze(abs(cwmcx(:,30,:)))'),[-1:0.5:8],'b-')
-contour(log10(abs(vi)),[-1:0.5:8],'r:')
-
-axis equal  
-set(gca,'xlim',[1 60])
-set(gca,'fontsize',20)
-xlabel('x (mm)')
-ylabel('z (mm)')
-legend('MCX','MMCM')
+%% -----------------------------------------------------------------
+figure;
+
+hold on;
+contour(log10(squeeze(abs(cwmcx(:, 30, :)))'), [-1:0.5:8], 'b-');
+contour(log10(abs(vi)), [-1:0.5:8], 'r:');
+
+axis equal;
+set(gca, 'xlim', [1 60]);
+set(gca, 'fontsize', 20);
+xlabel('x (mm)');
+ylabel('z (mm)');
+legend('MCX', 'MMCM');
 legend boxoff;
 box on;
 
-set(gcf,'PaperPositionMode','auto');
-saveas(gcf,'box.fig');
-
+set(gcf, 'PaperPositionMode', 'auto');
+saveas(gcf, 'box.fig');
diff --git a/examples/validation/tessmesh.m b/examples/validation/tessmesh.m
index 56be4798..b2c02134 100644
--- a/examples/validation/tessmesh.m
+++ b/examples/validation/tessmesh.m
@@ -1,12 +1,11 @@
-sessionid='cube2';
+sessionid = 'cube2';
 
 addpath('../../matlab/');
 
-[node,elem]=meshgrid6(0:60:60,0:60:60,0:60:60);
+[node, elem] = meshgrid6(0:60:60, 0:60:60, 0:60:60);
 
-elem(:,1:4)=meshreorient(node,elem(:,1:4));
-
-srcpos=[30.1,30.2,0];
-savemmcmesh(sessionid,node,elem,[]);
-eid=tsearchn(node,elem(:,1:4),srcpos)
+elem(:, 1:4) = meshreorient(node, elem(:, 1:4));
 
+srcpos = [30.1, 30.2, 0];
+savemmcmesh(sessionid, node, elem, []);
+eid = tsearchn(node, elem(:, 1:4), srcpos);
diff --git a/examples/widedet/createmesh.m b/examples/widedet/createmesh.m
index c246a992..83e9cb67 100644
--- a/examples/widedet/createmesh.m
+++ b/examples/widedet/createmesh.m
@@ -1,25 +1,24 @@
-
 %% original mesh
 
-[node,face,c0]=latticegrid([0 60],[0 60],[0 5 10]);
-c0(:,4)=[2;3];   % maximum element size for bottom (label 1) and top (label 2) layers
-[node,elem]=surf2mesh(node,face,[],[],1,[],c0);
+[node, face, c0] = latticegrid([0 60], [0 60], [0 5 10]);
+c0(:, 4) = [2; 3];   % maximum element size for bottom (label 1) and top (label 2) layers
+[node, elem] = surf2mesh(node, face, [], [], 1, [], c0);
 
 figure(1);
-plotmesh(node,elem);
+plotmesh(node, elem);
 
 srcpos = [25.0 35.0 10.0];
 
 %% extended detector domain
 
-detdef=struct('srctype','planar','srcpos',[10,10,-1],'srcdir',[0 0 1],...
-                'srcparam1',[40 0 0 40],'srcparam2',[0 40 0 40]);
-            
-[newnode,newelem]=mmcadddet(node,elem,detdef);
+detdef = struct('srctype', 'planar', 'srcpos', [10, 10, -1], 'srcdir', [0 0 1], ...
+                'srcparam1', [40 0 0 40], 'srcparam2', [0 40 0 40]);
+
+[newnode, newelem] = mmcadddet(node, elem, detdef);
 
 figure(2);
-plotmesh(newnode,newelem);
+plotmesh(newnode, newelem);
 
-newelem(:,1:4)=meshreorient(newnode,newelem(:,1:4));
-eid=tsearchn(newnode,newelem(:,1:4),srcpos)
-savemmcmesh('widedet',newnode,newelem);
\ No newline at end of file
+newelem(:, 1:4) = meshreorient(newnode, newelem(:, 1:4));
+eid = tsearchn(newnode, newelem(:, 1:4), srcpos);
+savemmcmesh('widedet', newnode, newelem);
diff --git a/examples/widedet/plot_results.m b/examples/widedet/plot_results.m
index bac5dfbb..bc5c6854 100644
--- a/examples/widedet/plot_results.m
+++ b/examples/widedet/plot_results.m
@@ -1,16 +1,16 @@
-
-nx = 40; ny=40;
+nx = 40;
+ny = 40;
 nTG = 50;
 
-fd=fopen('widedet.img','rb','ieee-le');
-data = fread(fd,nx*nx*nTG,'float');
-data=reshape(data,[nx ny nTG]);
+fd = fopen('widedet.img', 'rb', 'ieee-le');
+data = fread(fd, nx * nx * nTG, 'float');
+data = reshape(data, [nx ny nTG]);
 fclose(fd);
 
-datacw=sum(data,3);
+datacw = sum(data, 3);
 figure(1);
 imagesc(datacw');
 axis equal;
-xlim([0.5 nx+0.5]);
+xlim([0.5 nx + 0.5]);
 xlabel('offsetx (mm)');
 ylabel('offsety (mm)');
diff --git a/matlab/besselhprime.m b/matlab/besselhprime.m
index aa26f1eb..3b2e6905 100644
--- a/matlab/besselhprime.m
+++ b/matlab/besselhprime.m
@@ -1,8 +1,8 @@
-function hp=besselhprime(n,k,z)
+function hp = besselhprime(n, k, z)
 %
 % hp=besselhprime(n,k,z)
 %
-% Hankel function first order derivative 
+% Hankel function first order derivative
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
 %
@@ -12,7 +12,7 @@
 %     z: input variable
 %
 % output:
-%     hn: Hankel function first order derivative 
+%     hn: Hankel function first order derivative
 %
 % example:
 %     hn=besselhprime(0,1,1)
@@ -22,4 +22,4 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-hp=besselh(n-1,k,z)-n/z.*besselh(n,k,z);
+hp = besselh(n - 1, k, z) - n / z .* besselh(n, k, z);
diff --git a/matlab/besseljprime.m b/matlab/besseljprime.m
index 788a07be..97551d9b 100644
--- a/matlab/besseljprime.m
+++ b/matlab/besseljprime.m
@@ -1,8 +1,8 @@
-function jp=besseljprime(n,z)
+function jp = besseljprime(n, z)
 %
 % jp=besseljprime(n,z)
 %
-% Bessel function (Bessel first kind) first order derivative 
+% Bessel function (Bessel first kind) first order derivative
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
 %
@@ -21,4 +21,4 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-jp=besselj(n-1,z)-n/z.*besselj(n,z);
+jp = besselj(n - 1, z) - n / z .* besselj(n, z);
diff --git a/matlab/besselyprime.m b/matlab/besselyprime.m
index 071cf9c2..ca6172ee 100644
--- a/matlab/besselyprime.m
+++ b/matlab/besselyprime.m
@@ -1,8 +1,8 @@
-function yp=besselyprime(n,z)
+function yp = besselyprime(n, z)
 %
 % yp=besselyprime(n,z)
 %
-% Neumann function (Bessel second kind) first order derivative 
+% Neumann function (Bessel second kind) first order derivative
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
 %
@@ -11,7 +11,7 @@
 %     z: input variable
 %
 % output:
-%     yp: Neumann function (Bessel second kind) first order derivative 
+%     yp: Neumann function (Bessel second kind) first order derivative
 %
 % example:
 %     yp=besselyprime(0,1)
@@ -21,5 +21,4 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-
-yp=bessely(n-1,z)-n/z.*bessely(n,z);
+yp = bessely(n - 1, z) - n / z .* bessely(n, z);
diff --git a/matlab/cart2sphorigin.m b/matlab/cart2sphorigin.m
index f77b2050..8ef17a81 100644
--- a/matlab/cart2sphorigin.m
+++ b/matlab/cart2sphorigin.m
@@ -1,4 +1,4 @@
-function [T,P,R]=cart2sphorigin(xi,yi,zi,x0,y0,z0)
+function [T, P, R] = cart2sphorigin(xi, yi, zi, x0, y0, z0)
 %
 % [T,P,R]=cart2sphorigin(xi,yi,zi,x0,y0,z0)
 %
@@ -23,7 +23,7 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-xi=xi-x0;
-yi=yi-y0;
-zi=zi-z0;
-[T,P,R]=cart2sph(xi(:),yi(:),zi(:));
+xi = xi - x0;
+yi = yi - y0;
+zi = zi - z0;
+[T, P, R] = cart2sph(xi(:), yi(:), zi(:));
diff --git a/matlab/genT5mesh.m b/matlab/genT5mesh.m
index cea9e973..9d966d7b 100644
--- a/matlab/genT5mesh.m
+++ b/matlab/genT5mesh.m
@@ -1,70 +1,72 @@
-function [vertices,tess]=genT5mesh(varargin)
-% tess_lat: simplicial tessellation of a rectangular lattice
-% usage: [tessellation,vertices]=genT5mesh(v1,v2,v3,...)
-%
-% arguments: input
-% v1,v2,v3,... - numeric vectors defining the lattice in
-% each dimension.
-% Each vector must be of length >= 1
-%
-% arguments: (output)
-% vertices - factorial lattice created from (v1,v2,v3,...)
-% Each row of this array is one node in the lattice
-% tess - integer array defining simplexes as references to
-% rows of "vertices".
-
-% dimension of the lattice
-n = length(varargin);
-if(n~=3) error('only works for 3D case!'); end
-
-for i=1:n
-	v=varargin{i};
-	if(mod(length(v),2)==0)
-		varargin{i}=linspace(v(1),v(end),length(v)+1);
-	end
-end
-
-% create a single n-d hypercube
-% list of vertices of the cube itself
-
-cube8=...
-[1 4 5 13;1 2 5 11;1 10 11 13;11 13 14 5;11 13 1 5;...
- 2 3 5 11;3 5 6 15;15 11 12 3;15 11 14 5;11 15 3 5;...
- 4 5 7 13;5 7 8 17;16 17 13 7;13 17 14 5;5 7 17 13;...
- 5 6 9 15;5 8 9 17;17 18 15 9;17 15 14 5;17 15 5 9;...
- 10 13 11 19;13 11 14 23;22 19 23 13;19 23 20 11;13 11 19 23;...
- 11 12 15 21;11 15 14 23;23 21 20 11;23 24 21 15;23 21 11 15;...
- 16 13 17 25;13 17 14 23;25 26 23 17;25 22 23 13;13 17 25 23;...
- 17 18 15 27;17 15 14 23;26 27 23 17;27 23 24 15;23 27 17 15]';
-
-% build the complete lattice
-nodecount = cellfun('length',varargin);
-if any(nodecount<2)
-	error 'Each dimension must be of size 2 or more.'
-end
-vertices = lattice(varargin{:});
-
-[ix,iy,iz]=meshgrid(1:2:nodecount(1)-2,1:2:nodecount(2)-2,1:2:nodecount(3)-2);
-ind=sub2ind(nodecount,ix(:),iy(:),iz(:));
-
-nodeshift=[0 1 2 nodecount(1) nodecount(1)+1 nodecount(1)+2 ...
-2*nodecount(1) 2*nodecount(1)+1 2*nodecount(1)+2];
-nodeshift=[nodeshift,nodeshift+nodecount(1)*nodecount(2),nodeshift+2*nodecount(1)*nodecount(2)];
-
-nc=length(ind);
-tess=zeros(nc*40,4);
-for i=1:nc
-	tess((1:40)+(i-1)*40,:)=reshape(nodeshift(cube8(:)),4,40)'+ind(i);
-end
-
-% ======== subfunction ========
-function g = lattice(varargin)
-% generate a factorial lattice in n variables
-n=nargin;
-sizes = cellfun('length',varargin);
-c=cell(1,n);
-[c{1:n}]=ndgrid(varargin{:});
-g=zeros(prod(sizes),n);
-for i=1:n
-	g(:,i)=c{i}(:);
-end
+function [vertices, tess] = genT5mesh(varargin)
+% tess_lat: simplicial tessellation of a rectangular lattice
+% usage: [tessellation,vertices]=genT5mesh(v1,v2,v3,...)
+%
+% arguments: input
+% v1,v2,v3,... - numeric vectors defining the lattice in
+% each dimension.
+% Each vector must be of length >= 1
+%
+% arguments: (output)
+% vertices - factorial lattice created from (v1,v2,v3,...)
+% Each row of this array is one node in the lattice
+% tess - integer array defining simplexes as references to
+% rows of "vertices".
+
+% dimension of the lattice
+n = length(varargin);
+if (n ~= 3)
+    error('only works for 3D case!');
+end
+
+for i = 1:n
+    v = varargin{i};
+    if (mod(length(v), 2) == 0)
+        varargin{i} = linspace(v(1), v(end), length(v) + 1);
+    end
+end
+
+% create a single n-d hypercube
+% list of vertices of the cube itself
+
+cube8 = ...
+  [1 4 5 13; 1 2 5 11; 1 10 11 13; 11 13 14 5; 11 13 1 5; ...
+   2 3 5 11; 3 5 6 15; 15 11 12 3; 15 11 14 5; 11 15 3 5; ...
+   4 5 7 13; 5 7 8 17; 16 17 13 7; 13 17 14 5; 5 7 17 13; ...
+   5 6 9 15; 5 8 9 17; 17 18 15 9; 17 15 14 5; 17 15 5 9; ...
+   10 13 11 19; 13 11 14 23; 22 19 23 13; 19 23 20 11; 13 11 19 23; ...
+   11 12 15 21; 11 15 14 23; 23 21 20 11; 23 24 21 15; 23 21 11 15; ...
+   16 13 17 25; 13 17 14 23; 25 26 23 17; 25 22 23 13; 13 17 25 23; ...
+   17 18 15 27; 17 15 14 23; 26 27 23 17; 27 23 24 15; 23 27 17 15]';
+
+% build the complete lattice
+nodecount = cellfun('length', varargin);
+if any(nodecount < 2)
+    error 'Each dimension must be of size 2 or more.';
+end
+vertices = lattice(varargin{:});
+
+[ix, iy, iz] = meshgrid(1:2:nodecount(1) - 2, 1:2:nodecount(2) - 2, 1:2:nodecount(3) - 2);
+ind = sub2ind(nodecount, ix(:), iy(:), iz(:));
+
+nodeshift = [0 1 2 nodecount(1) nodecount(1) + 1 nodecount(1) + 2 ...
+             2 * nodecount(1) 2 * nodecount(1) + 1 2 * nodecount(1) + 2];
+nodeshift = [nodeshift, nodeshift + nodecount(1) * nodecount(2), nodeshift + 2 * nodecount(1) * nodecount(2)];
+
+nc = length(ind);
+tess = zeros(nc * 40, 4);
+for i = 1:nc
+    tess((1:40) + (i - 1) * 40, :) = reshape(nodeshift(cube8(:)), 4, 40)' + ind(i);
+end
+
+% ======== subfunction ========
+function g = lattice(varargin)
+% generate a factorial lattice in n variables
+n = nargin;
+sizes = cellfun('length', varargin);
+c = cell(1, n);
+[c{1:n}] = ndgrid(varargin{:});
+g = zeros(prod(sizes), n);
+for i = 1:n
+    g(:, i) = c{i}(:);
+end
diff --git a/matlab/genT6mesh.m b/matlab/genT6mesh.m
index a5fa9190..6e41a04d 100644
--- a/matlab/genT6mesh.m
+++ b/matlab/genT6mesh.m
@@ -1,67 +1,67 @@
-function [vertices,tess]=genT6mesh(varargin)
-% tess_lat: simplicial tessellation of a rectangular lattice
-% usage: [tessellation,vertices]=genT6mesh(v1,v2,v3,...)
-%
-% URL: http://www.mathkb.com/Uwe/Forum.aspx/matlab/50484/Constant-surfaces
-%
-% arguments: input
-% v1,v2,v3,... - numeric vectors defining the lattice in
-% each dimension.
-% Each vector must be of length >= 1
-%
-% arguments: (output)
-% vertices - factorial lattice created from (v1,v2,v3,...)
-% Each row of this array is one node in the lattice
-% tess - integer array defining simplexes as references to
-% rows of "vertices".
-
-% dimension of the lattice
-n = length(varargin);
-
-% create a single n-d hypercube
-% list of vertices of the cube itself
-vhc=('1'==dec2bin(0:(2^n-1)));
-% permutations of the integers 1:n
-p=perms(1:n);
-nt=factorial(n);
-thc=zeros(nt,n+1);
-for i=1:nt
-  thc(i,:)=find(all(diff(vhc(:,p(i,:)),[],2)>=0,2))';
-end
-
-% build the complete lattice
-nodecount = cellfun('length',varargin);
-if any(nodecount<2)
-  error 'Each dimension must be of size 2 or more.'
-end
-vertices = lattice(varargin{:});
-
-% unrolled index into each hyper-rectangle in the lattice
-ind = cell(1,n);
-for i=1:n
-ind{i} = 0:(nodecount(i)-2);
-end
-ind = lattice(ind{:});
-k = cumprod([1,nodecount(1:(end-1))]);
-ind = 1+ind*k';
-nind = length(ind);
-
-offset=vhc*k';
-tess=zeros(nt*nind,n+1);
-L=(1:nind)';
-for i=1:nt
-  tess(L,:)=repmat(ind,1,n+1)+repmat(offset(thc(i,:))',nind,1);
-L=L+nind;
-end
-
-% ======== subfunction ========
-function g = lattice(varargin)
-% generate a factorial lattice in n variables
-n=nargin;
-sizes = cellfun('length',varargin);
-c=cell(1,n);
-[c{1:n}]=ndgrid(varargin{:});
-g=zeros(prod(sizes),n);
-for i=1:n
-g(:,i)=c{i}(:);
-end
+function [vertices, tess] = genT6mesh(varargin)
+% tess_lat: simplicial tessellation of a rectangular lattice
+% usage: [tessellation,vertices]=genT6mesh(v1,v2,v3,...)
+%
+% URL: http://www.mathkb.com/Uwe/Forum.aspx/matlab/50484/Constant-surfaces
+%
+% arguments: input
+% v1,v2,v3,... - numeric vectors defining the lattice in
+% each dimension.
+% Each vector must be of length >= 1
+%
+% arguments: (output)
+% vertices - factorial lattice created from (v1,v2,v3,...)
+% Each row of this array is one node in the lattice
+% tess - integer array defining simplexes as references to
+% rows of "vertices".
+
+% dimension of the lattice
+n = length(varargin);
+
+% create a single n-d hypercube
+% list of vertices of the cube itself
+vhc = ('1' == dec2bin(0:(2^n - 1)));
+% permutations of the integers 1:n
+p = perms(1:n);
+nt = factorial(n);
+thc = zeros(nt, n + 1);
+for i = 1:nt
+    thc(i, :) = find(all(diff(vhc(:, p(i, :)), [], 2) >= 0, 2))';
+end
+
+% build the complete lattice
+nodecount = cellfun('length', varargin);
+if any(nodecount < 2)
+    error 'Each dimension must be of size 2 or more.';
+end
+vertices = lattice(varargin{:});
+
+% unrolled index into each hyper-rectangle in the lattice
+ind = cell(1, n);
+for i = 1:n
+    ind{i} = 0:(nodecount(i) - 2);
+end
+ind = lattice(ind{:});
+k = cumprod([1, nodecount(1:(end - 1))]);
+ind = 1 + ind * k';
+nind = length(ind);
+
+offset = vhc * k';
+tess = zeros(nt * nind, n + 1);
+L = (1:nind)';
+for i = 1:nt
+    tess(L, :) = repmat(ind, 1, n + 1) + repmat(offset(thc(i, :))', nind, 1);
+    L = L + nind;
+end
+
+% ======== subfunction ========
+function g = lattice(varargin)
+% generate a factorial lattice in n variables
+n = nargin;
+sizes = cellfun('length', varargin);
+c = cell(1, n);
+[c{1:n}] = ndgrid(varargin{:});
+g = zeros(prod(sizes), n);
+for i = 1:n
+    g(:, i) = c{i}(:);
+end
diff --git a/matlab/generate_g1.m b/matlab/generate_g1.m
index e1e145a8..0ba64473 100644
--- a/matlab/generate_g1.m
+++ b/matlab/generate_g1.m
@@ -1,4 +1,4 @@
-function [tau,g1]=generate_g1(fhist,tau, disp_model, DV, lambda, format, varargin)
+function [tau, g1] = generate_g1(fhist, tau, disp_model, DV, lambda, format, varargin)
 %
 %   [tau,g1]=generate_g1(fhist,tau, disp_model, DV, lambda, format)
 %
@@ -8,8 +8,8 @@
 %   author: Stefan Carp (carp <at> nmr.mgh.harvard.edu)
 %
 %   input:
-%       fhist:      the file name of the output .mch file 
-%       tau:        correlation times at which to compute g1 
+%       fhist:      the file name of the output .mch file
+%       tau:        correlation times at which to compute g1
 %                   (default: 1e-7 to 1e-1 seconds, log equidistant)
 %       disp_model: displacement model ('brownian', 'random_flow', <custom>)
 %                   (default: brownian, see further explanation below)
@@ -18,77 +18,86 @@
 %                   (default: 1e-7 mm^2/s, see further explanation below)
 %       lambda:     wavelenght of light used in nm
 %                   (default: 785)
-%       format:     the format used to save the .mch file 
+%       format:     the format used to save the .mch file
 %                   (default: 'float')
 %
 %   output:
 %
 %       tau:        correlation times at which g1 was computed provided for
-%                   convenience (copied from input if set, otherwise 
+%                   convenience (copied from input if set, otherwise
 %                   outputs default)
 %       g1:         field auto-correlation curves, one for each detector
 %
 %   The displacement model indicates the formula used to compute the root
 %   mean square displacement of scattering particles during a given delay
-%   
-%   brownian:       RMS= 6 * DV * tau; 
+%
+%   brownian:       RMS= 6 * DV * tau;
 %                   DV(displacement variable)=Db (brownian diffusion coeff)
-%   random_flow:    RMS= DV^2 * tau^2; 
+%   random_flow:    RMS= DV^2 * tau^2;
 %                   DV = V (first moment of velocity distribution)
 %   <custom>:       any string other than 'brownian' or 'random_flow' will
 %                   be evaluate as is using Matlab evalf, make sure it uses
 %                   'DV' as the flow related independent variable, tau is
-%                   indexed as tau(J). Any additional parameters can be 
+%                   indexed as tau(J). Any additional parameters can be
 %                   sent via "varargin"
 %
 %   This file is part of Mesh-Based Monte Carlo
 %   License: GPLv3, see http://mcx.sf.net for details
 %
 
-if nargin<6, format='float'; end
-if nargin<5, lambda=785; end
-if nargin<4, DV=1e-7; end
-if nargin<3, disp_model='brownian'; end
-if nargin<2, tau=logspace(-7,-1,200); end
+if nargin < 6
+    format = 'float';
+end
+if nargin < 5
+    lambda = 785;
+end
+if nargin < 4
+    DV = 1e-7;
+end
+if nargin < 3
+    disp_model = 'brownian';
+end
+if nargin < 2
+    tau = logspace(-7, -1, 200);
+end
 
-[mch_data,mch_header]=loadmch(fhist,format);
-temp=strfind(fhist,filesep);
-if isempty(temp), fhist=[pwd filesep fhist]; end
-temp=strfind(fhist,filesep);
-lastslash=temp(end);
-sim_label=fhist(lastslash+1:end-4);
+[mch_data, mch_header] = loadmch(fhist, format);
+temp = strfind(fhist, filesep);
+if isempty(temp)
+    fhist = [pwd filesep fhist];
+end
+temp = strfind(fhist, filesep);
+lastslash = temp(end);
+sim_label = fhist(lastslash + 1:end - 4);
 
-[mua,mus,g,n]=load_mc_prop([fhist(1:lastslash) filesep 'prop_' sim_label '.dat']);
+[mua, mus, g, n] = load_mc_prop([fhist(1:lastslash) filesep 'prop_' sim_label '.dat']);
 
-if (mch_header.recordnum-2)~=(2*mch_header.medianum),
+if (mch_header.recordnum - 2) ~= (2 * mch_header.medianum)
     fprintf('History file does not contain momentum transfer information \n');
-    g1=-1;
-    return;
+    g1 = -1;
+    return
 end
 
-if strcmp(disp_model,'brownian'),
-    disp_str='rmsdisp=6*DV.*tau(J);';
-elseif strcmp(disp_model,'random_flow'),
-    disp_str='rmsdisp=DV.^2.*tau(J).^2;';
-else 
-    disp_str=['rmsdisp=' disp_model ';'];
+if strcmp(disp_model, 'brownian')
+    disp_str = 'rmsdisp=6*DV.*tau(J);';
+elseif strcmp(disp_model, 'random_flow')
+    disp_str = 'rmsdisp=DV.^2.*tau(J).^2;';
+else
+    disp_str = ['rmsdisp=' disp_model ';'];
 end
 
-k0=2*pi*n/(lambda*1e-6);
+k0 = 2 * pi * n / (lambda * 1e-6);
 
-g1=zeros(mch_header.detnum,length(tau));
+g1 = zeros(mch_header.detnum, length(tau));
 
-for I=1:mch_header.detnum,
-    idx= find(mch_data(:,1)==I);     
-    fprintf('Processing detector %.0f: %.0f photons\n',I,length(idx));
+for I = 1:mch_header.detnum
+    idx = find(mch_data(:, 1) == I);
+    fprintf('Processing detector %.0f: %.0f photons\n', I, length(idx));
 
-    for J=1:length(tau),
+    for J = 1:length(tau)
         eval(disp_str);
-        g1(I,J)=sum(exp(-(k0.^2.*rmsdisp/3)*mch_data(idx,(3+mch_header.medianum):end)'-mua*mch_data(idx,3:(3+mch_header.medianum-1))'));
+        g1(I, J) = sum(exp(-(k0.^2 .* rmsdisp / 3) * mch_data(idx, (3 + mch_header.medianum):end)' - mua * mch_data(idx, 3:(3 + mch_header.medianum - 1))'));
     end
-    g1_norm=sum(exp(-mua*mch_data(idx,3:(3+mch_header.medianum-1))'));
-    g1(I,:)=g1(I,:)./g1_norm;
+    g1_norm = sum(exp(-mua * mch_data(idx, 3:(3 + mch_header.medianum - 1))'));
+    g1(I, :) = g1(I, :) ./ g1_norm;
 end
-    
-
-
diff --git a/matlab/load_mc_prop.m b/matlab/load_mc_prop.m
index 43b1974a..f4c9a74f 100644
--- a/matlab/load_mc_prop.m
+++ b/matlab/load_mc_prop.m
@@ -1,27 +1,28 @@
-function [mua,mus,g,n]=load_mc_prop(fname)
+function [mua, mus, g, n] = load_mc_prop(fname)
 %
 %   [mua,mus,g,n]=load_mc_prop(fname)
 %
-%   Loads the absorption and scattering coefficients, as well as the 
+%   Loads the absorption and scattering coefficients, as well as the
 %   scattering anisotropy and index of refraction from the MMC optical
 %   property file given as an argument
-%  
+%
 %   author: Stefan Carp (carp <at> nmr.mgh.harvard.edu
 
-
-fid=fopen(fname,'r');
-if fid<0, 
-  error('File %s not found\n',fname);
+fid = fopen(fname, 'r');
+if fid < 0
+    error('File %s not found\n', fname);
 end
 
-mc_version=fscanf(fid,'%f',1); if mc_version>1, fprintf('WARNING: MMC version greater than 1\n'); end
-num_tissues=fscanf(fid,'%f',1);
-
-for I=1:num_tissues,
-    tiss_ind=fscanf(fid,'%f',1);
-    mua(tiss_ind)=fscanf(fid,'%f',1);
-    mus(tiss_ind)=fscanf(fid,'%f',1);
-    g(tiss_ind)=fscanf(fid,'%f',1);
-    n(tiss_ind)=fscanf(fid,'%f',1);
+mc_version = fscanf(fid, '%f', 1);
+if mc_version > 1
+    fprintf('WARNING: MMC version greater than 1\n');
 end
+num_tissues = fscanf(fid, '%f', 1);
 
+for I = 1:num_tissues
+    tiss_ind = fscanf(fid, '%f', 1);
+    mua(tiss_ind) = fscanf(fid, '%f', 1);
+    mus(tiss_ind) = fscanf(fid, '%f', 1);
+    g(tiss_ind) = fscanf(fid, '%f', 1);
+    n(tiss_ind) = fscanf(fid, '%f', 1);
+end
diff --git a/matlab/loadmch.m b/matlab/loadmch.m
index 2e988f43..92bfa92c 100644
--- a/matlab/loadmch.m
+++ b/matlab/loadmch.m
@@ -1,4 +1,4 @@
-function [data, headerstruct, photonseed]=loadmch(fname,format,endian)
+function [data, headerstruct, photonseed] = loadmch(fname, format, endian)
 %
 %    [data, header]=loadmch(fname,format,endian)
 %
@@ -13,8 +13,8 @@
 %
 %    output:
 %        data:   the output detected photon data array
-%                data has at least M*2+2 columns (M=header.medium), the first column is the 
-%                ID of the detector; columns 2 to M+1 store the number of 
+%                data has at least M*2+2 columns (M=header.medium), the first column is the
+%                ID of the detector; columns 2 to M+1 store the number of
 %                scattering events for every tissue region; the following M
 %                columns are the partial path lengths (in mm) for each medium type;
 %                the last column is the initial weight at launch time of each detecetd
@@ -29,8 +29,8 @@
 %                [version,medianum,detnum,recordnum,totalphoton,detectedphoton,
 %                 savedphoton,lengthunit,seedbyte,normalizer,respin,srcnum,savedetflag]
 %        photonseed: (optional) if the mch file contains a seed section, this
-%                returns the seed data for each detected photon. Each row of 
-%                photonseed is a byte array, which can be used to initialize a  
+%                returns the seed data for each detected photon. Each row of
+%                photonseed is a byte array, which can be used to initialize a
 %                seeded simulation. Note that the seed is RNG specific. You must use
 %                the an identical RNG to utilize these seeds for a new simulation.
 %
@@ -38,81 +38,83 @@
 %    License: GPLv3, see http://mcx.sf.net for details
 %
 
-if(nargin==1)
-   format='float32=>float32';
+if (nargin == 1)
+    format = 'float32=>float32';
 end
 
-if(nargin<3)
-   endian='ieee-le';
+if (nargin < 3)
+    endian = 'ieee-le';
 end
 
-fid=fopen(fname,'rb',endian);
+fid = fopen(fname, 'rb', endian);
 
-data=[];
-header=[];
-photonseed=[];
+data = [];
+header = [];
+photonseed = [];
 
-while(~feof(fid))
-	magicheader=fread(fid,4,'char');
-	if(strcmp(char(magicheader(:))','MCXH')~=1)
-		if(isempty(header))
-			fclose(fid);
-			error('can not find a MCX history data block');
-		end
-		break;
-	end
-	hd=fread(fid,7,'uint'); % version, maxmedia, detnum, colcount, totalphoton, detected, savedphoton
-	if(hd(1)~=1) error('version higher than 1 is not supported'); end
-    unitmm=fread(fid,1,'float32');
-	seedbyte=fread(fid,1,'uint');
-    normalizer=fread(fid,1,'float32');
-	respin=fread(fid,1,'int');
-	srcnum=fread(fid,1,'uint');
-	savedetflag=fread(fid,1,'uint');
-	junk=fread(fid,2,'uint');
+while (~feof(fid))
+    magicheader = fread(fid, 4, 'char');
+    if (strcmp(char(magicheader(:))', 'MCXH') ~= 1)
+        if (isempty(header))
+            fclose(fid);
+            error('can not find a MCX history data block');
+        end
+        break
+    end
+    hd = fread(fid, 7, 'uint'); % version, maxmedia, detnum, colcount, totalphoton, detected, savedphoton
+    if (hd(1) ~= 1)
+        error('version higher than 1 is not supported');
+    end
+    unitmm = fread(fid, 1, 'float32');
+    seedbyte = fread(fid, 1, 'uint');
+    normalizer = fread(fid, 1, 'float32');
+    respin = fread(fid, 1, 'int');
+    srcnum = fread(fid, 1, 'uint');
+    savedetflag = fread(fid, 1, 'uint');
+    junk = fread(fid, 2, 'uint');
 
-    detflag=dec2bin(bitand(savedetflag,63))-'0';
-    datalen=[1 hd(2) hd(2) hd(2) 3 3 1];
-    datlen=detflag.*datalen(1:length(detflag));
+    detflag = dec2bin(bitand(savedetflag, 63)) - '0';
+    datalen = [1 hd(2) hd(2) hd(2) 3 3 1];
+    datlen = detflag .* datalen(1:length(detflag));
 
-    dat=fread(fid,hd(7)*hd(4),format);
-    dat=reshape(dat,[hd(4),hd(7)])';
-    if(savedetflag && length(detflag)>2 && detflag(3)>0)
-	    dat(:,sum(datlen(1:2))+1:sum(datlen(1:3)))=dat(:,sum(datlen(1:2))+1:sum(datlen(1:3)))*unitmm;
-    elseif(savedetflag==0)
-        dat(:,2+hd(2):(1+2*hd(2)))=dat(:,2+hd(2):(1+2*hd(2)))*unitmm;
+    dat = fread(fid, hd(7) * hd(4), format);
+    dat = reshape(dat, [hd(4), hd(7)])';
+    if (savedetflag && length(detflag) > 2 && detflag(3) > 0)
+        dat(:, sum(datlen(1:2)) + 1:sum(datlen(1:3))) = dat(:, sum(datlen(1:2)) + 1:sum(datlen(1:3))) * unitmm;
+    elseif (savedetflag == 0)
+        dat(:, 2 + hd(2):(1 + 2 * hd(2))) = dat(:, 2 + hd(2):(1 + 2 * hd(2))) * unitmm;
     end
-	data=[data;dat];
-        if(seedbyte>0)
-            try
-              seeds=fread(fid,hd(7)*seedbyte,'uchar');
-              seeds=reshape(seeds,[seedbyte,hd(7)])';
-              photonseed=[photonseed;seeds];
-            catch
-              seedbyte=0;
-              warning('photon seed section is not found');
-            end
+    data = [data; dat];
+    if (seedbyte > 0)
+        try
+            seeds = fread(fid, hd(7) * seedbyte, 'uchar');
+            seeds = reshape(seeds, [seedbyte, hd(7)])';
+            photonseed = [photonseed; seeds];
+        catch
+            seedbyte = 0;
+            warning('photon seed section is not found');
         end
-	if(respin>1)
-	    hd(5)=hd(5)*respin;
-	end
-	if(isempty(header))
-		header=[hd;unitmm]';
-	else
-		if(any(header([1:4 8])~=[hd([1:4])' unitmm]))
-			error('loadmch can only load data generated from a single session');
-		else
-			header(5:7)=header(5:7)+hd(5:7)';
-		end
-	end
+    end
+    if (respin > 1)
+        hd(5) = hd(5) * respin;
+    end
+    if (isempty(header))
+        header = [hd; unitmm]';
+    else
+        if (any(header([1:4 8]) ~= [hd([1:4])' unitmm]))
+            error('loadmch can only load data generated from a single session');
+        else
+            header(5:7) = header(5:7) + hd(5:7)';
+        end
+    end
 end
 
 fclose(fid);
 
-if(nargout>=2)
-   headerstruct=struct('version',header(1),'medianum',header(2),'detnum',header(3),...
-                       'recordnum',header(4),'totalphoton',header(5),...
-                       'detectedphoton',header(6),'savedphoton',header(7),...
-                       'lengthunit',header(8),'seedbyte',seedbyte,'normalizer',normalizer,...
-		       'respin',respin,'srcnum',srcnum,'savedetflag',savedetflag);
+if (nargout >= 2)
+    headerstruct = struct('version', header(1), 'medianum', header(2), 'detnum', header(3), ...
+                          'recordnum', header(4), 'totalphoton', header(5), ...
+                          'detectedphoton', header(6), 'savedphoton', header(7), ...
+                          'lengthunit', header(8), 'seedbyte', seedbyte, 'normalizer', normalizer, ...
+                          'respin', respin, 'srcnum', srcnum, 'savedetflag', savedetflag);
 end
diff --git a/matlab/mmcadddet.m b/matlab/mmcadddet.m
index 64ffa3ce..7a7cbc7d 100644
--- a/matlab/mmcadddet.m
+++ b/matlab/mmcadddet.m
@@ -1,4 +1,4 @@
-function varargout=mmcadddet(varargin)
+function varargout = mmcadddet(varargin)
 %
 % [newnode,newelem]=mmcadddet(node,elem,det,opt)
 %   or
@@ -37,5 +37,4 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-[varargout{1:nargout}]=mmcaddsrc(varargin{:},'extcorelabel',-2,'KeepShape',1,'Expansion',1.0);
-
+[varargout{1:nargout}] = mmcaddsrc(varargin{:}, 'extcorelabel', -2, 'KeepShape', 1, 'Expansion', 1.0);
diff --git a/matlab/mmcaddsrc.m b/matlab/mmcaddsrc.m
index a7f60e79..a63cb173 100644
--- a/matlab/mmcaddsrc.m
+++ b/matlab/mmcaddsrc.m
@@ -1,4 +1,4 @@
-function [newnode,newelem]=mmcaddsrc(node,elem,src,varargin)
+function [newnode, newelem] = mmcaddsrc(node, elem, src, varargin)
 %
 % [newnode,newelem]=mmcaddsrc(node,elem,src,opt)
 %   or
@@ -21,7 +21,7 @@
 %              the opt struct can be replaced by a list of 'param','value' pairs
 %
 % output:
-%     newnode: the node list of the modified mesh, by default, 
+%     newnode: the node list of the modified mesh, by default,
 %              newnode is a concatination of src at the end of node
 %     newelem: the elem list of the modified mesh, by default, the elements
 %              between the convex hull of the combined node/src and
@@ -60,12 +60,12 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-opt=varargin2struct(varargin{:});
-if(~isfield(opt,'extcmdopt'))
-   opt.extcmdopt='-Y';
+opt = varargin2struct(varargin{:});
+if (~isfield(opt, 'extcmdopt'))
+    opt.extcmdopt = '-Y';
 end
-if(isstruct(src))
-    src=mmcsrcdomain(src,[min(node);max(node)],opt);
+if (isstruct(src))
+    src = mmcsrcdomain(src, [min(node); max(node)], opt);
 end
-opt.newnode=src;
-[newnode,newelem]=meshrefine(node,elem,opt);
+opt.newnode = src;
+[newnode, newelem] = meshrefine(node, elem, opt);
diff --git a/matlab/mmcdettime.m b/matlab/mmcdettime.m
index b08d0e23..7a0bcf1d 100644
--- a/matlab/mmcdettime.m
+++ b/matlab/mmcdettime.m
@@ -1,17 +1,17 @@
-function dett=mmcdettime(detp,prop,unitinmm)
+function dett = mmcdettime(detp, prop, unitinmm)
 %
 % dett=mmcdettime(detp,prop,unitinmm)
 %
-% Recalculate the detected photon time using partial path data and 
+% Recalculate the detected photon time using partial path data and
 % optical properties (for perturbation Monte Carlo or detector readings)
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
-%	  Ruoyang Yao (yaor <at> rpi.edu) 
+%     Ruoyang Yao (yaor <at> rpi.edu)
 %
 % input:
 %     detp: the 2nd output from mmclab. detp must be a struct
 %     prop: optical property list, as defined in the cfg.prop field of mmclab's input
-%     unitinmm: voxel edge-length in mm, should use cfg.unitinmm used to generate detp; 
+%     unitinmm: voxel edge-length in mm, should use cfg.unitinmm used to generate detp;
 %           if ignored, assume to be 1 (mm)
 %
 % output:
@@ -22,33 +22,33 @@
 % License: GPLv3, see http://mmc.space/ for details
 %
 
-R_C0 = 3.335640951981520e-12;	% inverse of light speed in vacuum
+R_C0 = 3.335640951981520e-12;   % inverse of light speed in vacuum
 
-if(nargin<3)
-    if(isfield(detp,'unitinmm'))
-        unitinmm=detp.unitinmm;
+if (nargin < 3)
+    if (isfield(detp, 'unitinmm'))
+        unitinmm = detp.unitinmm;
     else
-        unitinmm=1;
+        unitinmm = 1;
     end
 end
 
-if(nargin<2)
-    if(isfield(detp,'prop'))
-        prop=detp.prop;
+if (nargin < 2)
+    if (isfield(detp, 'prop'))
+        prop = detp.prop;
     else
         error('must provide input "prop"');
     end
 end
 
-medianum=size(prop,1);
-if(medianum<=1)
+medianum = size(prop, 1);
+if (medianum <= 1)
     error('empty property list');
 end
 
-if(isstruct(detp))
-    dett=zeros(size(detp.ppath,1),1);
-    for i=1:medianum-1
-        dett=dett+prop(i+1,4)*detp.ppath(:,i)*R_C0*unitinmm;
+if (isstruct(detp))
+    dett = zeros(size(detp.ppath, 1), 1);
+    for i = 1:medianum - 1
+        dett = dett + prop(i + 1, 4) * detp.ppath(:, i) * R_C0 * unitinmm;
     end
 else
     error('the first input must be a struct with a subfield named "ppath"');
diff --git a/matlab/mmcdettpsf.m b/matlab/mmcdettpsf.m
index 35d6c00c..79b2d49a 100644
--- a/matlab/mmcdettpsf.m
+++ b/matlab/mmcdettpsf.m
@@ -1,4 +1,4 @@
-function tpsf = mmcdettpsf(detp,detnum,prop,time)
+function tpsf = mmcdettpsf(detp, detnum, prop, time)
 %
 % tpsf=mmcdettpsf(detp,detnum,prop,time)
 %
@@ -6,7 +6,7 @@
 % given the partial path data, optical properties, and distribution of time bins
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
-%	  Ruoyang Yao (yaor <at> rpi.edu) 
+%     Ruoyang Yao (yaor <at> rpi.edu)
 %
 % input:
 %     detp: the 2nd output from mmclab. detp must be a struct
@@ -23,25 +23,25 @@
 %
 
 % select the photon data of the specified detector
-detp.ppath=detp.ppath(detp.detid==detnum,:);
-detp.detid=detp.detid(detp.detid==detnum);
+detp.ppath = detp.ppath(detp.detid == detnum, :);
+detp.detid = detp.detid(detp.detid == detnum);
 
 % calculate the detected photon weight and arrival time
-replayweight=mmcdetweight(detp,prop);
-replaytime=mmcdettime(detp,prop);
+replayweight = mmcdetweight(detp, prop);
+replaytime = mmcdettime(detp, prop);
 
 % define temporal point spread function vector
-nTG = round((time(2)-time(1))/time(3));     % maximum time gate number
-tpsf = zeros(nTG,1);
+nTG = round((time(2) - time(1)) / time(3));     % maximum time gate number
+tpsf = zeros(nTG, 1);
 
 % calculate the time bin, make sure not to exceed the boundary
-ntg = ceil((replaytime-time(1))/time(3));
-ntg(ntg<1)=1;
-ntg(ntg>nTG)=nTG;
+ntg = ceil((replaytime - time(1)) / time(3));
+ntg(ntg < 1) = 1;
+ntg(ntg > nTG) = nTG;
 
 % add each photon weight to corresponding time bin
-for i=1:length(replayweight)
-    tpsf(ntg(i)) = tpsf(ntg(i))+replayweight(i);
+for i = 1:length(replayweight)
+    tpsf(ntg(i)) = tpsf(ntg(i)) + replayweight(i);
 end
 
 end
diff --git a/matlab/mmcdetweight.m b/matlab/mmcdetweight.m
index f4838486..f65843fa 100644
--- a/matlab/mmcdetweight.m
+++ b/matlab/mmcdetweight.m
@@ -1,16 +1,16 @@
-function detw=mmcdetweight(detp,prop,unitinmm)
+function detw = mmcdetweight(detp, prop, unitinmm)
 %
 % detw=mmcdetweight(detp,prop,unitinmm)
 %
-% Recalculate the detected photon weight using partial path data and 
+% Recalculate the detected photon weight using partial path data and
 % optical properties (for perturbation Monte Carlo or detector readings)
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
 %
 % input:
-%     detp: the 2nd output from mmclab. detp must a struct 
+%     detp: the 2nd output from mmclab. detp must a struct
 %     prop: optical property list, as defined in the cfg.prop field of mmclab's input
-%     unitinmm: voxel edge-length in mm, should use cfg.unitinmm used to generate detp; 
+%     unitinmm: voxel edge-length in mm, should use cfg.unitinmm used to generate detp;
 %           if ignored, assume to be 1 (mm)
 %
 % output:
@@ -21,35 +21,35 @@
 % License: GPLv3, see http://mmc.space/ for details
 %
 
-if(nargin<2)
-    if(isfield(detp,'prop'))
-        prop=detp.prop;
+if (nargin < 2)
+    if (isfield(detp, 'prop'))
+        prop = detp.prop;
     else
         error('must provide input "prop"');
     end
 end
 
-medianum=size(prop,1);
-if(medianum<=1)
+medianum = size(prop, 1);
+if (medianum <= 1)
     error('empty property list');
 end
 
-if(nargin<3)
-    if(isfield(detp,'unitinmm'))
-        unitinmm=detp.unitinmm;
+if (nargin < 3)
+    if (isfield(detp, 'unitinmm'))
+        unitinmm = detp.unitinmm;
     else
-        unitinmm=1;
+        unitinmm = 1;
     end
 end
 
-if(isstruct(detp))
-    if(~isfield(detp,'w0'))
-        detw=ones(size(detp.ppath,1),1);
+if (isstruct(detp))
+    if (~isfield(detp, 'w0'))
+        detw = ones(size(detp.ppath, 1), 1);
     else
-        detw=detp.w0;
+        detw = detp.w0;
     end
-    for i=1:medianum-1
-        detw=detw.*exp(-prop(i+1,1)*detp.ppath(:,i)*unitinmm);
+    for i = 1:medianum - 1
+        detw = detw .* exp(-prop(i + 1, 1) * detp.ppath(:, i) * unitinmm);
     end
 else
     error('the first input must be a struct with a subfield named "ppath"');
diff --git a/matlab/mmcjacobian.m b/matlab/mmcjacobian.m
index aee4d562..79b9b68e 100644
--- a/matlab/mmcjacobian.m
+++ b/matlab/mmcjacobian.m
@@ -1,9 +1,9 @@
-function [Jmua, Jmus]=mmcjacobian(cfg,detp,seeds,detnum)
+function [Jmua, Jmus] = mmcjacobian(cfg, detp, seeds, detnum)
 %
 % [Jmua, Jmus]=mmcjacobian(cfg,detp,seeds,detnum) (element based)
 %
-% Generate time-domain Jacobians (sensitivity matrix) for absorption and scattering (mus) 
-% perturbation of a specified source-detector pair with configurations, detected photon 
+% Generate time-domain Jacobians (sensitivity matrix) for absorption and scattering (mus)
+% perturbation of a specified source-detector pair with configurations, detected photon
 % seeds and detector readings from an initial MC simulation
 %
 % author: Ruoyang Yao (yaor <at> rpi.edu)
@@ -19,20 +19,20 @@
 %     Jmua: the Jacobian for absorption coefficient for a specified source-detector pair
 %           also output Jmua as a by-product.
 %     Jmus: (optional) the Jacobian for scattering perturbation of a specified source detector pair
-%		  number of rows is the number of the mesh elements
-%		  number of columns is the number of time gates
+%         number of rows is the number of the mesh elements
+%         number of columns is the number of time gates
 %
 % example:
-%	  [cube,detp,ncfg,seeds]=mmclab(cfg);            % initial MC simulation
-%	  [Jmua,Jmus] = mmcjacobian(ncfg,detp,seeds,1);  % generate scattering Jacobian of the first detector
+%     [cube,detp,ncfg,seeds]=mmclab(cfg);            % initial MC simulation
+%     [Jmua,Jmus] = mmcjacobian(ncfg,detp,seeds,1);  % generate scattering Jacobian of the first detector
 %
 % this file is part of Mesh-based Monte Carlo (MMC)
 %
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-if(nargout==1)
-    Jmua=mmcjmua(cfg,detp,seeds,detnum);
-elseif(nargout==2)
-    [Jmus,Jmua]=mmcjmus(cfg,detp,seeds,detnum);
+if (nargout == 1)
+    Jmua = mmcjmua(cfg, detp, seeds, detnum);
+elseif (nargout == 2)
+    [Jmus, Jmua] = mmcjmus(cfg, detp, seeds, detnum);
 end
diff --git a/matlab/mmcjmua.m b/matlab/mmcjmua.m
index 8f2309a0..17ec8900 100644
--- a/matlab/mmcjmua.m
+++ b/matlab/mmcjmua.m
@@ -1,4 +1,4 @@
-function [Ja, newcfg]=mmcjmua(cfg,detp,seeds,detnum)
+function [Ja, newcfg] = mmcjmua(cfg, detp, seeds, detnum)
 %
 % Ja=mmcjmua(cfg,detp,seeds,detnum) (element based)
 %
@@ -11,18 +11,18 @@
 % input:
 %     cfg: the simulation configuration structure used for the initial MC simulation by mmclab
 %     detp: detector readings from the initial MC simulation, must be a
-%	        structure (supported after MMC v2016.4)
+%           structure (supported after MMC v2016.4)
 %     seeds: detected photon seeds from the initial MC simulation
 %     detnum: the detector number whose detected photons will be replayed
 %
 % output:
 %     Ja: a Jacobian for absorption perturbation of the specified detector
-%		  number of rows is the number of the mesh nodes or elements
-%		  number of columns is the number of time gates
+%         number of rows is the number of the mesh nodes or elements
+%         number of columns is the number of time gates
 %
 % example:
-%	  [cube,detp,ncfg,seeds]=mmclab(cfg);	% initial MC simulation
-%	  Jmua = mmcjmua(ncfg,detp,seeds,1);    % generate absorption Jacobian of the first detector
+%     [cube,detp,ncfg,seeds]=mmclab(cfg);   % initial MC simulation
+%     Jmua = mmcjmua(ncfg,detp,seeds,1);    % generate absorption Jacobian of the first detector
 %
 % this file is part of Mesh-based Monte Carlo (MMC)
 %
@@ -30,31 +30,31 @@
 %
 
 % preprocessing of the mesh to get possible missing fields
-newcfg=mmclab(cfg,'prep');
-%newcfg.basisorder=0;
+newcfg = mmclab(cfg, 'prep');
+% newcfg.basisorder=0;
 
 % specify the detector number to replay
-newcfg.replaydet=detnum;
+newcfg.replaydet = detnum;
 
 % select the photon seeds and data of the specified detector
-newcfg.seed=seeds.data(:,detp.detid==newcfg.replaydet);
-detp.data=detp.data(:,detp.detid==newcfg.replaydet);
+newcfg.seed = seeds.data(:, detp.detid == newcfg.replaydet);
+detp.data = detp.data(:, detp.detid == newcfg.replaydet);
 
 % calculate the detected photon weight and arrival time
-newcfg.replayweight=mmcdetweight(detp.data,newcfg.prop);
-newcfg.replaytime=mmcdettime(detp.data,newcfg.prop);
+newcfg.replayweight = mmcdetweight(detp.data, newcfg.prop);
+newcfg.replaytime = mmcdettime(detp.data, newcfg.prop);
 
 % specify output type
-newcfg.isnormalized=1; % should we leave this for users to decide?
-newcfg.outputtype='wl';
+newcfg.isnormalized = 1; % should we leave this for users to decide?
+newcfg.outputtype = 'wl';
 
 % now replay detected photons
-[jacob,detp1,newcfg]=mmclab(newcfg);
+[jacob, detp1, newcfg] = mmclab(newcfg);
 
 % validate if the replay is successful
-if(all(ismember(round(detp1.data'*1e10)*1e-10,round(detp.data'*1e10)*1e-10,'rows')))
-	% disp('replay is successful :-)');
-	Ja=-jacob.data;
+if (all(ismember(round(detp1.data' * 1e10) * 1e-10, round(detp.data' * 1e10) * 1e-10, 'rows')))
+    % disp('replay is successful :-)');
+    Ja = -jacob.data;
 else
-	error('replay failed :-(');
+    error('replay failed :-(');
 end
diff --git a/matlab/mmcjmus.m b/matlab/mmcjmus.m
index bede7c4d..0fa3c9be 100644
--- a/matlab/mmcjmus.m
+++ b/matlab/mmcjmus.m
@@ -1,4 +1,4 @@
-function [Jmus, Jmua]=mmcjmus(cfg,detp,seeds,detnum)
+function [Jmus, Jmua] = mmcjmus(cfg, detp, seeds, detnum)
 %
 % [Jmus, Jmua]=mmcjmus(cfg,detp,seeds,detnum) (element based)
 %
@@ -16,57 +16,57 @@
 %
 % output:
 %     Jmus: the Jacobian for scattering perturbation of a specified source detector pair
-%		  number of rows is the number of the mesh elements
-%		  number of columns is the number of time gates
+%         number of rows is the number of the mesh elements
+%         number of columns is the number of time gates
 %     Jmua: (optional) because calculating Jmus requires the Jacobian for mua, so one can
 %           also output Jmua as a by-product.
 %
 % example:
-%	  [cube,detp,ncfg,seeds]=mmclab(cfg);   % initial MC simulation
-%	  Jmus = mmcjmus(ncfg,detp,seeds,1);    % generate scattering Jacobian of the first detector
+%     [cube,detp,ncfg,seeds]=mmclab(cfg);   % initial MC simulation
+%     Jmus = mmcjmus(ncfg,detp,seeds,1);    % generate scattering Jacobian of the first detector
 %
 % this file is part of Mesh-based Monte Carlo (MMC)
 %
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-[Jmua, newcfg]=mmcjmua(cfg,detp,seeds,detnum);
+[Jmua, newcfg] = mmcjmua(cfg, detp, seeds, detnum);
 
 % specify output type 2
-newcfg.outputtype='wp';
+newcfg.outputtype = 'wp';
 
 % replay detected photons for weighted partialpath
-[jacob,detp2]=mmclab(newcfg);
+[jacob, detp2] = mmclab(newcfg);
 
 % generate a map for scattering coefficient
-elemp=newcfg.elemprop;
-idx=find(elemp>0);
-elemp(elemp<0)=0;
-musmap0=newcfg.prop(elemp+1,2);
+elemp = newcfg.elemprop;
+idx = find(elemp > 0);
+elemp(elemp < 0) = 0;
+musmap0 = newcfg.prop(elemp + 1, 2);
 
-if(newcfg.basisorder==1)
-    dim=4;
-    nodemus=zeros(size(newcfg.node,1),1);
-    nodevol=zeros(size(newcfg.node,1),1);
-    for i=1:length(idx)
-       nodemus(newcfg.elem(idx(i),1:dim))=nodemus(newcfg.elem(idx(i),1:dim))+newcfg.evol(idx(i))*musmap0(idx(i));
-       nodevol(newcfg.elem(idx(i),1:dim))=nodevol(newcfg.elem(idx(i),1:dim))+newcfg.evol(idx(i));
+if (newcfg.basisorder == 1)
+    dim = 4;
+    nodemus = zeros(size(newcfg.node, 1), 1);
+    nodevol = zeros(size(newcfg.node, 1), 1);
+    for i = 1:length(idx)
+        nodemus(newcfg.elem(idx(i), 1:dim)) = nodemus(newcfg.elem(idx(i), 1:dim)) + newcfg.evol(idx(i)) * musmap0(idx(i));
+        nodevol(newcfg.elem(idx(i), 1:dim)) = nodevol(newcfg.elem(idx(i), 1:dim)) + newcfg.evol(idx(i));
     end
-    musmap=nodemus./nodevol;
-    musmap(isnan(musmap))=newcfg.prop(1,2);
+    musmap = nodemus ./ nodevol;
+    musmap(isnan(musmap)) = newcfg.prop(1, 2);
 else
-    musmap=musmap0;
+    musmap = musmap0;
 end
 
 % divide by local scattering coefficient
-jacob.data=jacob.data./repmat(musmap(:),1,size(jacob.data,2));
-jacob.data(musmap<0)=0;
+jacob.data = jacob.data ./ repmat(musmap(:), 1, size(jacob.data, 2));
+jacob.data(musmap < 0) = 0;
 
 % validate if the replay is successful
 
-if(all(ismember(round(detp2.data'*1e10)*1e-10,round(detp.data'*1e10)*1e-10,'rows')))
-	%disp('replay is successful :-)');
-	Jmus=Jmua+jacob.data;
+if (all(ismember(round(detp2.data' * 1e10) * 1e-10, round(detp.data' * 1e10) * 1e-10, 'rows')))
+    % disp('replay is successful :-)');
+    Jmus = Jmua + jacob.data;
 else
-	error('replay failed :-(');
+    error('replay failed :-(');
 end
diff --git a/matlab/mmcmeanpath.m b/matlab/mmcmeanpath.m
index b64933da..d58b473b 100644
--- a/matlab/mmcmeanpath.m
+++ b/matlab/mmcmeanpath.m
@@ -1,4 +1,4 @@
-function avgpath=mmcmeanpath(detp,prop)
+function avgpath = mmcmeanpath(detp, prop)
 %
 % avgpath=mmcmeanpath(detp,prop)
 %
@@ -11,12 +11,12 @@
 %     prop: optical property list, as defined in the cfg.prop field of mmclab's input
 %
 % output:
-%     avepath: the average pathlength for each tissue type 
+%     avepath: the average pathlength for each tissue type
 %
 % this file is part of Mesh-based Monte Carlo (MMC)
 %
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-detw=mmcdetweight(detp,prop);
-avgpath=sum(detp.ppath.*repmat(detw(:),1,size(detp.ppath,2))) / sum(detw(:));
+detw = mmcdetweight(detp, prop);
+avgpath = sum(detp.ppath .* repmat(detw(:), 1, size(detp.ppath, 2))) / sum(detw(:));
diff --git a/matlab/mmcmeanscat.m b/matlab/mmcmeanscat.m
index a0a30714..bda18160 100644
--- a/matlab/mmcmeanscat.m
+++ b/matlab/mmcmeanscat.m
@@ -1,4 +1,4 @@
-function avgnscat=mmcmeanscat(detp,prop)
+function avgnscat = mmcmeanscat(detp, prop)
 %
 % avgnscat=mmcmeanscat(detp,prop)
 %
@@ -11,12 +11,12 @@
 %     prop: optical property list, as defined in the cfg.prop field of mmclab's input
 %
 % output:
-%     avgnscat: the average scattering event count for each tissue type 
+%     avgnscat: the average scattering event count for each tissue type
 %
 % this file is part of Mesh-based Monte Carlo (MMC)
 %
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-detw=mmcdetweight(detp,prop);
-avgnscat=sum(detp.nscat.*repmat(detw(:),1,size(detp.ppath,2))) / sum(detw(:));
+detw = mmcdetweight(detp, prop);
+avgnscat = sum(detp.nscat .* repmat(detw(:), 1, size(detp.ppath, 2))) / sum(detw(:));
diff --git a/matlab/mmcraytrace.m b/matlab/mmcraytrace.m
index 9b563b96..dd355c75 100644
--- a/matlab/mmcraytrace.m
+++ b/matlab/mmcraytrace.m
@@ -1,4 +1,4 @@
-function [p,e0]=mmcraytrace(node,elem,p0,v0,e0)
+function [p, e0] = mmcraytrace(node, elem, p0, v0, e0)
 %
 % [p,e0]=mmcraytrace(node,elem,p0,v0,e0)
 %
@@ -22,53 +22,55 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-p=p0;
-if(size(elem,2)==3)
-    face=elem;
+p = p0;
+if (size(elem, 2) == 3)
+    face = elem;
 else
-    face=volface(elem);
+    face = volface(elem);
 end
-[t,u,v,idx]=raytrace(p0,v0,node,face);
-if(isempty(idx))
+[t, u, v, idx] = raytrace(p0, v0, node, face);
+if (isempty(idx))
     error('ray does not intersect with the mesh');
 else
-    t=t(idx);
-    if(e0=='>')
-        idx1=find(t>=0);
-    elseif(e0=='<')
-        idx1=find(t<=0);
-    elseif(isnan(e0) || e0=='-')
-        idx1=1:length(t);
+    t = t(idx);
+    if (e0 == '>')
+        idx1 = find(t >= 0);
+    elseif (e0 == '<')
+        idx1 = find(t <= 0);
+    elseif (isnan(e0) || e0 == '-')
+        idx1 = 1:length(t);
     else
         error('ray direction specifier is not recognized');
     end
-    if(isempty(idx1))
+    if (isempty(idx1))
         error('no intersection is found along the ray direction');
     end
-    t0=abs(t(idx1));
-    [tmin,loc]=min(t0);
-    faceidx=idx(idx1(loc));
+    t0 = abs(t(idx1));
+    [tmin, loc] = min(t0);
+    faceidx = idx(idx1(loc));
 
     % update source position
-    p=p0+t(idx1(loc))*v0;
+    p = p0 + t(idx1(loc)) * v0;
 
-    if(nargout<2)
-        return;
+    if (nargout < 2)
+        return
     end
 
     % find initial element id
-    if(size(elem,2)==3)
-        e0=faceidx;
+    if (size(elem, 2) == 3)
+        e0 = faceidx;
     else
-       felem=sort(face(faceidx,:));
-       f=elem;
-       f=[f(:,[1,2,3]);
-          f(:,[2,1,4]);
-          f(:,[1,3,4]);
-          f(:,[2,4,3])];
-       [tf,loc]=ismember(felem,sort(f,2),'rows');
-       loc=mod(loc,size(elem,1));
-       if(loc==0) loc=size(elem,1); end
-       e0=loc;
+        felem = sort(face(faceidx, :));
+        f = elem;
+        f = [f(:, [1, 2, 3])
+             f(:, [2, 1, 4])
+             f(:, [1, 3, 4])
+             f(:, [2, 4, 3])];
+        [tf, loc] = ismember(felem, sort(f, 2), 'rows');
+        loc = mod(loc, size(elem, 1));
+        if (loc == 0)
+            loc = size(elem, 1);
+        end
+        e0 = loc;
     end
 end
diff --git a/matlab/mmcsrcdomain.m b/matlab/mmcsrcdomain.m
index f61428d8..50497031 100644
--- a/matlab/mmcsrcdomain.m
+++ b/matlab/mmcsrcdomain.m
@@ -1,8 +1,8 @@
-function [srcnode,srcface]=mmcsrcdomain(cfg,meshbbx,varargin)
+function [srcnode, srcface] = mmcsrcdomain(cfg, meshbbx, varargin)
 %
 % [srcnode,srcface]=mmcsrcdomain(cfg)
 %
-% Defining a source domain (for launching new photons) in the form of 
+% Defining a source domain (for launching new photons) in the form of
 % polyhedra based on an MMCLAB simulation configuration structure
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
@@ -38,67 +38,67 @@
 % the launching domain should be slightly larger than the actual source
 % domain to avoid starting from an edge or vertex
 
-opt=varargin2struct(varargin{:});
-expansion=jsonopt('Expansion',1.1,opt); 
-rotateangle=jsonopt('Rotate',0.0,opt); 
+opt = varargin2struct(varargin{:});
+expansion = jsonopt('Expansion', 1.1, opt);
+rotateangle = jsonopt('Rotate', 0.0, opt);
 
-if(~isstruct(cfg))
-   error('input cfg must be a struct');
+if (~isstruct(cfg))
+    error('input cfg must be a struct');
 end
-if(~isfield(cfg,'srcpos') || ~isfield(cfg,'srcdir') || ...
-   ~isfield(cfg,'srctype') )
+if (~isfield(cfg, 'srcpos') || ~isfield(cfg, 'srcdir') || ...
+    ~isfield(cfg, 'srctype'))
     error('you must at least define cfg.srcpos, cfg.srcdir, cfg.srctype');
 end
 
-if(strcmp(cfg.srctype,'isotropic'))
-    cfg.srcdir(1:3)=rand(1,3);
-    cfg.srcdir(1:3)=cfg.srcdir(1:3)/norm(cfg.srcdir(1:3));
+if (strcmp(cfg.srctype, 'isotropic'))
+    cfg.srcdir(1:3) = rand(1, 3);
+    cfg.srcdir(1:3) = cfg.srcdir(1:3) / norm(cfg.srcdir(1:3));
 end
-cfg.srcdir(1:3)=cfg.srcdir(1:3)/norm(cfg.srcdir(1:3));
-domainradius=min(meshbbx(2,:)-meshbbx(1,:))*0.25;
-domaindiagnoal=norm(meshbbx(2,:)-meshbbx(1,:));
-if(strcmp(cfg.srctype,'pencil'))
-   warning(['for external pencil beams, you are highly recommended to set ' ...
-       'cfg.e0=''>'', instead of using this script']); 
+cfg.srcdir(1:3) = cfg.srcdir(1:3) / norm(cfg.srcdir(1:3));
+domainradius = min(meshbbx(2, :) - meshbbx(1, :)) * 0.25;
+domaindiagnoal = norm(meshbbx(2, :) - meshbbx(1, :));
+if (strcmp(cfg.srctype, 'pencil'))
+    warning(['for external pencil beams, you are highly recommended to set ' ...
+             'cfg.e0=''>'', instead of using this script']);
 end
 
-vperp=cross(cfg.srcdir(1:3),rand(1,3));
+vperp = cross(cfg.srcdir(1:3), rand(1, 3));
 
-if(strcmp(cfg.srctype,'pencil') || strcmp(cfg.srctype,'cone') || ...
-        strcmp(cfg.srctype,'zgaussian')|| strcmp(cfg.srctype,'isotropic') || strcmp(cfg.srctype,'arcsine'))
-    srcnode=orthdisk(cfg.srcpos,cfg.srcpos+cfg.srcdir(1:3),domainradius,3,vperp,rotateangle);
-    srcface=[1 2 3];
-elseif(strcmp(cfg.srctype,'gaussian'))
-    srcnode=orthdisk(cfg.srcpos,cfg.srcpos+cfg.srcdir(1:3),domaindiagnoal*0.5,3,vperp,rotateangle);
-    srcface=[1 2 3];
-elseif(strcmp(cfg.srctype,'line') || strcmp(cfg.srctype,'slit'))
-    v0=cfg.srcpos+cfg.srcparam1(1:3)*0.5;
-    srcnode=orthdisk(v0,v0+cfg.srcdir(1:3),norm(cfg.srcparam1(1:3))*expansion,3,cfg.srcparam1(1:3));
-    srcface=[1 2 3];
-elseif(strcmp(cfg.srctype,'planar') || strcmp(cfg.srctype,'pattern') || ...
-        strcmp(cfg.srctype,'fourier') ||strcmp(cfg.srctype,'fourierx')||strcmp(cfg.srctype,'fourier2d'))
-    v0=cfg.srcpos(1:3);
-    v1=cfg.srcparam1(1:3);
-    v2=cfg.srcparam2(1:3);
-    if(strcmp(cfg.srctype,'fourierx')||strcmp(cfg.srctype,'fourier2d'))
-        v2=cross(v0,v1);
+if (strcmp(cfg.srctype, 'pencil') || strcmp(cfg.srctype, 'cone') || ...
+    strcmp(cfg.srctype, 'zgaussian') || strcmp(cfg.srctype, 'isotropic') || strcmp(cfg.srctype, 'arcsine'))
+    srcnode = orthdisk(cfg.srcpos, cfg.srcpos + cfg.srcdir(1:3), domainradius, 3, vperp, rotateangle);
+    srcface = [1 2 3];
+elseif (strcmp(cfg.srctype, 'gaussian'))
+    srcnode = orthdisk(cfg.srcpos, cfg.srcpos + cfg.srcdir(1:3), domaindiagnoal * 0.5, 3, vperp, rotateangle);
+    srcface = [1 2 3];
+elseif (strcmp(cfg.srctype, 'line') || strcmp(cfg.srctype, 'slit'))
+    v0 = cfg.srcpos + cfg.srcparam1(1:3) * 0.5;
+    srcnode = orthdisk(v0, v0 + cfg.srcdir(1:3), norm(cfg.srcparam1(1:3)) * expansion, 3, cfg.srcparam1(1:3));
+    srcface = [1 2 3];
+elseif (strcmp(cfg.srctype, 'planar') || strcmp(cfg.srctype, 'pattern') || ...
+        strcmp(cfg.srctype, 'fourier') || strcmp(cfg.srctype, 'fourierx') || strcmp(cfg.srctype, 'fourier2d'))
+    v0 = cfg.srcpos(1:3);
+    v1 = cfg.srcparam1(1:3);
+    v2 = cfg.srcparam2(1:3);
+    if (strcmp(cfg.srctype, 'fourierx') || strcmp(cfg.srctype, 'fourier2d'))
+        v2 = cross(v0, v1);
     end
-    voff1=(v1+v2)*0.5;
-    voff2=(v1-v2)*0.5;
-    if(jsonopt('KeepShape',0,opt))
-        srcnode=[v0; v0+v1; v0+v1+v2; v0+v2]+[-voff1; voff2; voff1; -voff2]*(expansion-1.0);
-        srcface=[1 2 3;3 4 1];
+    voff1 = (v1 + v2) * 0.5;
+    voff2 = (v1 - v2) * 0.5;
+    if (jsonopt('KeepShape', 0, opt))
+        srcnode = [v0; v0 + v1; v0 + v1 + v2; v0 + v2] + [-voff1; voff2; voff1; -voff2] * (expansion - 1.0);
+        srcface = [1 2 3; 3 4 1];
     else
-        srcnode=orthdisk(cfg.srcpos+voff1,cfg.srcpos+voff1+cfg.srcdir(1:3),(max(norm(voff1),norm(voff2)))*2.0*expansion,3,v1+v2,rotateangle);
-        srcface=[1 2 3];
+        srcnode = orthdisk(cfg.srcpos + voff1, cfg.srcpos + voff1 + cfg.srcdir(1:3), (max(norm(voff1), norm(voff2))) * 2.0 * expansion, 3, v1 + v2, rotateangle);
+        srcface = [1 2 3];
     end
-elseif(strcmp(cfg.srctype,'disk'))
-    if(jsonopt('KeepShape',0,opt))
-        srcnode=orthdisk(cfg.srcpos,cfg.srcpos+cfg.srcdir(1:3),cfg.srcparam1(1)*expansion,jsonopt('CircleDiv',100,opt));
-        srcface=delaunay(srcnode(:,1),srcnode(:,2));
+elseif (strcmp(cfg.srctype, 'disk'))
+    if (jsonopt('KeepShape', 0, opt))
+        srcnode = orthdisk(cfg.srcpos, cfg.srcpos + cfg.srcdir(1:3), cfg.srcparam1(1) * expansion, jsonopt('CircleDiv', 100, opt));
+        srcface = delaunay(srcnode(:, 1), srcnode(:, 2));
     else
-        srcnode=orthdisk(cfg.srcpos,cfg.srcpos+cfg.srcdir(1:3),(cfg.srcparam1(1)*2.0)*expansion,3,vperp,rotateangle);
-        srcface=[1 2 3];
+        srcnode = orthdisk(cfg.srcpos, cfg.srcpos + cfg.srcdir(1:3), (cfg.srcparam1(1) * 2.0) * expansion, 3, vperp, rotateangle);
+        srcface = [1 2 3];
     end
 else
     error(['source type not supported: ', cfg.srctype]);
diff --git a/matlab/readmmcelem.m b/matlab/readmmcelem.m
index c7ae7bf5..acc2aeb9 100644
--- a/matlab/readmmcelem.m
+++ b/matlab/readmmcelem.m
@@ -1,4 +1,4 @@
-function elem=readmmcelem(filename)
+function elem = readmmcelem(filename)
 %
 % elem=readmmcelem(filename)
 %
@@ -10,7 +10,7 @@
 %     filename: the file name to the element data file
 %
 % output:
-%     elem: the tetrahedral mesh element list 
+%     elem: the tetrahedral mesh element list
 %
 % example:
 %     elem=readmmcelem('elem_sph1.dat');
@@ -20,10 +20,10 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-fid=fopen(filename,'rt');
-[header,c]=fscanf(fid,'%d',2);
-elem=fscanf(fid,'%d',[6 header(2)]);
+fid = fopen(filename, 'rt');
+[header, c] = fscanf(fid, '%d', 2);
+elem = fscanf(fid, '%d', [6 header(2)]);
 fclose(fid);
 
-elem=elem';
-elem=elem(:,2:end);
+elem = elem';
+elem = elem(:, 2:end);
diff --git a/matlab/readmmcface.m b/matlab/readmmcface.m
index f16c6938..e3e13391 100644
--- a/matlab/readmmcface.m
+++ b/matlab/readmmcface.m
@@ -1,4 +1,4 @@
-function face=readmmcface(filename)
+function face = readmmcface(filename)
 %
 % face=readmmcface(filename)
 %
@@ -10,7 +10,7 @@
 %     filename: the file name to the surface element data file
 %
 % output:
-%     face: the surface triangle element list 
+%     face: the surface triangle element list
 %
 % example:
 %     face=readmmcface('face_sph1.dat');
@@ -20,10 +20,10 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-fid=fopen(filename,'rt');
-[header,c]=fscanf(fid,'%d',2);
-face=fscanf(fid,'%d',[5 header(2)]);
+fid = fopen(filename, 'rt');
+[header, c] = fscanf(fid, '%d', 2);
+face = fscanf(fid, '%d', [5 header(2)]);
 fclose(fid);
 
-face=face';
-face=face(:,2:4);
+face = face';
+face = face(:, 2:4);
diff --git a/matlab/readmmcmesh.m b/matlab/readmmcmesh.m
index 4e7b7b34..36133b42 100644
--- a/matlab/readmmcmesh.m
+++ b/matlab/readmmcmesh.m
@@ -1,33 +1,33 @@
-function varargout=readmmcmesh(key)
-%
-% [node elem]=readmmcmesh(key)
-%
-% Loading MMC node and element data files
-%
-% author: Qianqian Fang (q.fang <at> neu.edu)
-%
-% input:
-%     key: the file name stub to the node coordinate file. The full 
-%          file names are {node,elem}_key.dat
-%
-% output:
-%     node: the node coordinate list
-%     elem: the tetrahedra node index list
-%
-% example:
-%     [node elem]=readmmcmesh('sph1');
-%
-% this file is part of Mesh-based Monte Carlo (MMC)
-%
-% License: GPLv3, see http://mcx.sf.net/mmc/ for details
-%
-
-if(nargout>=1)
-    varargout{1}=readmmcnode(['node_',key,'.dat']);
-end
-if(nargout>=2)
-    varargout{2}=readmmcelem(['elem_',key,'.dat']);
-end
-if(nargout>=3)
-    varargout{3}=readmmcelem(['elem_',key,'.dat']);
-end
+function varargout = readmmcmesh(key)
+%
+% [node elem]=readmmcmesh(key)
+%
+% Loading MMC node and element data files
+%
+% author: Qianqian Fang (q.fang <at> neu.edu)
+%
+% input:
+%     key: the file name stub to the node coordinate file. The full
+%          file names are {node,elem}_key.dat
+%
+% output:
+%     node: the node coordinate list
+%     elem: the tetrahedra node index list
+%
+% example:
+%     [node elem]=readmmcmesh('sph1');
+%
+% this file is part of Mesh-based Monte Carlo (MMC)
+%
+% License: GPLv3, see http://mcx.sf.net/mmc/ for details
+%
+
+if (nargout >= 1)
+    varargout{1} = readmmcnode(['node_', key, '.dat']);
+end
+if (nargout >= 2)
+    varargout{2} = readmmcelem(['elem_', key, '.dat']);
+end
+if (nargout >= 3)
+    varargout{3} = readmmcelem(['elem_', key, '.dat']);
+end
diff --git a/matlab/readmmcnode.m b/matlab/readmmcnode.m
index cc71186a..07a602c6 100644
--- a/matlab/readmmcnode.m
+++ b/matlab/readmmcnode.m
@@ -1,29 +1,29 @@
-function node=readmmcnode(filename)
-%
-% node=readmmcnode(filename)
-%
-% Loading MMC node coordinates data file
-%
-% author: Qianqian Fang (q.fang <at> neu.edu)
-%
-% input:
-%     filename: the file name to the node coordinate file
-%
-% output:
-%     node: the node coordinate list 
-%
-% example:
-%     node=readmmcnode('node_sph1.dat');
-%
-% this file is part of Mesh-based Monte Carlo (MMC)
-%
-% License: GPLv3, see http://mcx.sf.net/mmc/ for details
-%
-
-fid=fopen(filename,'rt');
-hd=fscanf(fid,'%d',2);
-node=fscanf(fid,'%d %e %e %e\n',hd(2)*4);
-fclose(fid);
-
-node=reshape(node,[4,hd(2)])';
-node=node(:,2:4);
+function node = readmmcnode(filename)
+%
+% node=readmmcnode(filename)
+%
+% Loading MMC node coordinates data file
+%
+% author: Qianqian Fang (q.fang <at> neu.edu)
+%
+% input:
+%     filename: the file name to the node coordinate file
+%
+% output:
+%     node: the node coordinate list
+%
+% example:
+%     node=readmmcnode('node_sph1.dat');
+%
+% this file is part of Mesh-based Monte Carlo (MMC)
+%
+% License: GPLv3, see http://mcx.sf.net/mmc/ for details
+%
+
+fid = fopen(filename, 'rt');
+hd = fscanf(fid, '%d', 2);
+node = fscanf(fid, '%d %e %e %e\n', hd(2) * 4);
+fclose(fid);
+
+node = reshape(node, [4, hd(2)])';
+node = node(:, 2:4);
diff --git a/matlab/savemmcmesh.m b/matlab/savemmcmesh.m
index a27b66f3..c0757a1f 100644
--- a/matlab/savemmcmesh.m
+++ b/matlab/savemmcmesh.m
@@ -1,4 +1,4 @@
-function savemmcmesh(key,node,elem,varargin)
+function savemmcmesh(key, node, elem, varargin)
 %
 % savemmcmesh(key,node,elem,face,evol,facenb)
 % savemmcmesh(key,node,elem,'face',face,'evol',evol,'facenb',facenb,'roi',roi)
@@ -8,7 +8,7 @@ function savemmcmesh(key,node,elem,varargin)
 % author: Qianqian Fang (q.fang <at> neu.edu)
 %
 % input:
-%     key: a string included in all exported mesh file names, the 
+%     key: a string included in all exported mesh file names, the
 %          format of the files are {node,elem,face,facenb,evol}_key.dat
 %      node: a node coordinate list, 3 columns for x/y/z
 %      elem: a tetrahedral element list
@@ -27,78 +27,78 @@ function savemmcmesh(key,node,elem,varargin)
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-opt=varargin2struct(varargin{:});
+opt = varargin2struct(varargin{:});
 
-if(nargin<5 || isempty(jsonopt('evol',[],opt)))
-  evol=elemvolume(node,elem(:,1:4));
+if (nargin < 5 || isempty(jsonopt('evol', [], opt)))
+    evol = elemvolume(node, elem(:, 1:4));
 end
 
-if(~isempty(node))
-  fid=fopen(['node_',key,'.dat'],'wt');
-  fprintf(fid,'%d\t%d\n',1,size(node,1));
-  fprintf(fid,'%d\t%16.8e\t%16.8e\t%16.8e\n',[1:length(node);node']);
-  fclose(fid);
+if (~isempty(node))
+    fid = fopen(['node_', key, '.dat'], 'wt');
+    fprintf(fid, '%d\t%d\n', 1, size(node, 1));
+    fprintf(fid, '%d\t%16.8e\t%16.8e\t%16.8e\n', [1:length(node); node']);
+    fclose(fid);
 end
 
-if(~isempty(elem))
-  elem(:,1:4)=meshreorient(node,elem(:,1:4));
+if (~isempty(elem))
+    elem(:, 1:4) = meshreorient(node, elem(:, 1:4));
 
-  fid=fopen(['elem_',key,'.dat'],'wt');
-  fprintf(fid,'%d\t%d\n',1,size(elem,1));
-  if(size(elem,2)==4)
-    fprintf(fid,'%d\t%d\t%d\t%d\t%d\t1\n', [1:length(elem);elem']);
-  elseif(size(elem,2)==5)
-    fprintf(fid,'%d\t%d\t%d\t%d\t%d\t%d\n',[1:length(elem);elem']);
-  else
+    fid = fopen(['elem_', key, '.dat'], 'wt');
+    fprintf(fid, '%d\t%d\n', 1, size(elem, 1));
+    if (size(elem, 2) == 4)
+        fprintf(fid, '%d\t%d\t%d\t%d\t%d\t1\n', [1:length(elem); elem']);
+    elseif (size(elem, 2) == 5)
+        fprintf(fid, '%d\t%d\t%d\t%d\t%d\t%d\n', [1:length(elem); elem']);
+    else
+        fclose(fid);
+        error('wrong elem input: must be 4 or 5 columns');
+    end
     fclose(fid);
-    error('wrong elem input: must be 4 or 5 columns');
-  end
-  fclose(fid);
 end
 
-if(~isempty(jsonopt('facenb',[],opt)))
-    facenb=jsonopt('facenb',[],opt);
+if (~isempty(jsonopt('facenb', [], opt)))
+    facenb = jsonopt('facenb', [], opt);
 end
-if(nargin<6 || isempty(jsonopt('facenb',[],opt)))
-  facenb=faceneighbors(elem(:,1:4));
-  if(nargin<4 || isempty(jsonopt('face',[],opt)))
-     face=faceneighbors(elem(:,1:4),'rowmajor');
-  end
+if (nargin < 6 || isempty(jsonopt('facenb', [], opt)))
+    facenb = faceneighbors(elem(:, 1:4));
+    if (nargin < 4 || isempty(jsonopt('face', [], opt)))
+        face = faceneighbors(elem(:, 1:4), 'rowmajor');
+    end
 end
 
-if(~isempty(face))
-  fid=fopen(['face_',key,'.dat'],'wt');
-  fprintf(fid,'%d\t%d\n',1,size(face,1));
-  if(size(face,2)==3)
-    fprintf(fid,'%d\t%d\t%d\t%d\t1\n',[1:length(face);face']);
-  elseif(size(face,2)==4)
-    fprintf(fid,'%d\t%d\t%d\t%d\t%d\n',[1:length(face);face']);
-  else
+if (~isempty(face))
+    fid = fopen(['face_', key, '.dat'], 'wt');
+    fprintf(fid, '%d\t%d\n', 1, size(face, 1));
+    if (size(face, 2) == 3)
+        fprintf(fid, '%d\t%d\t%d\t%d\t1\n', [1:length(face); face']);
+    elseif (size(face, 2) == 4)
+        fprintf(fid, '%d\t%d\t%d\t%d\t%d\n', [1:length(face); face']);
+    else
+        fclose(fid);
+        error('wrong face input: must be 3 or 4 columns');
+    end
     fclose(fid);
-    error('wrong face input: must be 3 or 4 columns');
-  end
-  fclose(fid);
 end
 
-if(~isempty(evol))
-  fid=fopen(['velem_' key '.dat'],'wt');
-  fprintf(fid,'%d %d\n',1,size(elem,1));
-  fprintf(fid,'%d %e\n',[(1:size(elem,1))',evol]');
-  fclose(fid);
+if (~isempty(evol))
+    fid = fopen(['velem_' key '.dat'], 'wt');
+    fprintf(fid, '%d %d\n', 1, size(elem, 1));
+    fprintf(fid, '%d %e\n', [(1:size(elem, 1))', evol]');
+    fclose(fid);
 end
 
-if(~isempty(facenb))
-  fid=fopen(['facenb_' key '.dat'],'wt');
-  fprintf(fid,'%d %d\n',1,size(elem,1));
-  fprintf(fid,'%d\t%d\t%d\t%d\n',facenb');
-  fclose(fid);
+if (~isempty(facenb))
+    fid = fopen(['facenb_' key '.dat'], 'wt');
+    fprintf(fid, '%d %d\n', 1, size(elem, 1));
+    fprintf(fid, '%d\t%d\t%d\t%d\n', facenb');
+    fclose(fid);
 end
 
-roi=jsonopt('roi',[],opt);
-if(~isempty(roi))
-  fid=fopen(['roi_' key '.dat'],'wt');
-  fprintf(fid,'%d %d\n',size(roi,2),size(roi,1));
-  format=[repmat('%d\t',1,size(roi,2)) '\n'];
-  fprintf(fid,format,roi');
-  fclose(fid);
-end
\ No newline at end of file
+roi = jsonopt('roi', [], opt);
+if (~isempty(roi))
+    fid = fopen(['roi_' key '.dat'], 'wt');
+    fprintf(fid, '%d %d\n', size(roi, 2), size(roi, 1));
+    format = [repmat('%d\t', 1, size(roi, 2)) '\n'];
+    fprintf(fid, format, roi');
+    fclose(fid);
+end
diff --git a/matlab/spbesselh.m b/matlab/spbesselh.m
index 4960be33..f13841de 100644
--- a/matlab/spbesselh.m
+++ b/matlab/spbesselh.m
@@ -1,8 +1,8 @@
-function hn=spbesselh(n,k,z)
+function hn = spbesselh(n, k, z)
 %
 % hn=spbesselhprime(n,k,z)
 %
-% spherical Hankel function 
+% spherical Hankel function
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
 %
@@ -12,7 +12,7 @@
 %     z: input variable
 %
 % output:
-%     hn: spherical Hankel function 
+%     hn: spherical Hankel function
 %
 % example:
 %     hn=spbesselh(0,1,1)
@@ -22,10 +22,10 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-if(k==1)
-    hn=spbesselj(n,z)+i*spbessely(n,z);
-elseif(k==2)
-    hn=spbesselj(n,z)-i*spbessely(n,z);
+if (k == 1)
+    hn = spbesselj(n, z) + i * spbessely(n, z);
+elseif (k == 2)
+    hn = spbesselj(n, z) - i * spbessely(n, z);
 else
     error('wrong value for the second parameter');
 end
diff --git a/matlab/spbesselhprime.m b/matlab/spbesselhprime.m
index 7e2e527c..5433908a 100644
--- a/matlab/spbesselhprime.m
+++ b/matlab/spbesselhprime.m
@@ -1,8 +1,8 @@
-function hn=spbesselhprime(n,k,z)
+function hn = spbesselhprime(n, k, z)
 %
 % hn=spbesselhprime(n,k,z)
 %
-% spherical Hankel function first order derivative 
+% spherical Hankel function first order derivative
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
 %
@@ -12,7 +12,7 @@
 %     z: input variable
 %
 % output:
-%     hn: spherical Hankel function first order derivative 
+%     hn: spherical Hankel function first order derivative
 %
 % example:
 %     hn=spbesselhprime(0,1,1)
@@ -22,10 +22,10 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-if(k==1)
-    hn=spbesseljprime(n,z)+i*spbesselyprime(n,z);
-elseif(k==2)
-    hn=spbesseljprime(n,z)-i*spbesselyprime(n,z);
+if (k == 1)
+    hn = spbesseljprime(n, z) + i * spbesselyprime(n, z);
+elseif (k == 2)
+    hn = spbesseljprime(n, z) - i * spbesselyprime(n, z);
 else
     error('wrong value for the second parameter');
 end
diff --git a/matlab/spbesselj.m b/matlab/spbesselj.m
index 8e0fbaec..d450b6ce 100644
--- a/matlab/spbesselj.m
+++ b/matlab/spbesselj.m
@@ -1,4 +1,4 @@
-function jn=spbesselj(n,z)
+function jn = spbesselj(n, z)
 %
 % jn=spbesselj(n,z)
 %
@@ -21,4 +21,4 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-jn=besselj(n+1/2,z).*sqrt(pi./(2*z));
+jn = besselj(n + 1 / 2, z) .* sqrt(pi ./ (2 * z));
diff --git a/matlab/spbesseljprime.m b/matlab/spbesseljprime.m
index 7a2d1358..dfc87049 100644
--- a/matlab/spbesseljprime.m
+++ b/matlab/spbesseljprime.m
@@ -1,4 +1,4 @@
-function jp=spbesseljprime(n,z)
+function jp = spbesseljprime(n, z)
 %
 % jp=spbesseljprime(n,z)
 %
@@ -21,4 +21,4 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-jp=besseljprime(n+1/2,z).*sqrt(pi/(2*z))-sqrt(pi/2)*besselj(n+1/2,z)./(2*z.*sqrt(z));
+jp = besseljprime(n + 1 / 2, z) .* sqrt(pi / (2 * z)) - sqrt(pi / 2) * besselj(n + 1 / 2, z) ./ (2 * z .* sqrt(z));
diff --git a/matlab/spbessely.m b/matlab/spbessely.m
index 7698557e..3b8df5cf 100644
--- a/matlab/spbessely.m
+++ b/matlab/spbessely.m
@@ -1,8 +1,8 @@
-function yn=spbessely(n,z)
+function yn = spbessely(n, z)
 %
 % yn=spbessely(n,z)
 %
-% spherical Neumann function 
+% spherical Neumann function
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
 %
@@ -11,7 +11,7 @@
 %     z: input variable
 %
 % output:
-%     yn:  spherical Neumann function first order derivative 
+%     yn:  spherical Neumann function first order derivative
 %
 % example:
 %     yn=spbessely(0,1)
@@ -21,4 +21,4 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-yn=bessely(n+1/2,z).*sqrt(pi./(2*z));
+yn = bessely(n + 1 / 2, z) .* sqrt(pi ./ (2 * z));
diff --git a/matlab/spbesselyprime.m b/matlab/spbesselyprime.m
index 50620fc3..49927524 100644
--- a/matlab/spbesselyprime.m
+++ b/matlab/spbesselyprime.m
@@ -1,8 +1,8 @@
-function yp=spbesselyprime(n,z)
+function yp = spbesselyprime(n, z)
 %
 % yp=spbesselyprime(n,z)
 %
-% spherical Neumann function first order derivative 
+% spherical Neumann function first order derivative
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
 %
@@ -11,7 +11,7 @@
 %     z: input variable
 %
 % output:
-%     yp:  spherical Neumann function first order derivative 
+%     yp:  spherical Neumann function first order derivative
 %
 % example:
 %     yp=spbesselyprime(0,1)
@@ -21,4 +21,4 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-yp=besselyprime(n+1/2,z).*sqrt(pi/(2*z))-sqrt(pi/2)*bessely(n+1/2,z)./(2*z.*sqrt(z));
+yp = besselyprime(n + 1 / 2, z) .* sqrt(pi / (2 * z)) - sqrt(pi / 2) * bessely(n + 1 / 2, z) ./ (2 * z .* sqrt(z));
diff --git a/matlab/spharmonic.m b/matlab/spharmonic.m
index f6c6c140..b3f7a2eb 100644
--- a/matlab/spharmonic.m
+++ b/matlab/spharmonic.m
@@ -1,4 +1,4 @@
-function Y=spharmonic(l,m,theta,phi)
+function Y = spharmonic(l, m, theta, phi)
 %
 % Y=spharmonic(l,m,theta,phi)
 %
@@ -22,17 +22,17 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-coeff=1;
-oldm=m;
-if(m<0)
-    coeff=(-1)^m*prod(1:(l-m))/prod(1:(l+m));
-    m=-m;
+coeff = 1;
+oldm = m;
+if (m < 0)
+    coeff = (-1)^m * prod(1:(l - m)) / prod(1:(l + m));
+    m = -m;
 end
-Lmn=legendre(l,cos((theta(:))'));
-if l~=0
-  Lmn=squeeze(Lmn(m+1,:))';
+Lmn = legendre(l, cos((theta(:))'));
+if l ~= 0
+    Lmn = squeeze(Lmn(m + 1, :))';
 end
-Lmn=reshape(Lmn,size(theta));
-m=oldm;
-Y=coeff*sqrt((2*l+1)*prod(1:(l-m))/(prod(1:(l+m))*4*pi)) ...
-  *Lmn.*exp(i*m*phi);
+Lmn = reshape(Lmn, size(theta));
+m = oldm;
+Y = coeff * sqrt((2 * l + 1) * prod(1:(l - m)) / (prod(1:(l + m)) * 4 * pi)) * ...
+   Lmn .* exp(i * m * phi);
diff --git a/matlab/sphdiffAcoeff.m b/matlab/sphdiffAcoeff.m
index 1cb330c6..9ccd42fa 100644
--- a/matlab/sphdiffAcoeff.m
+++ b/matlab/sphdiffAcoeff.m
@@ -1,4 +1,4 @@
-function A=sphdiffAcoeff(m,l,cfg)
+function A = sphdiffAcoeff(m, l, cfg)
 %
 % A=sphdiffAcoeff(m,l,cfg)
 %
@@ -22,14 +22,14 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-if((cfg.src(2)==pi | cfg.src(2)==0) & m~=0)
-    A=0;
-    return;
+if ((cfg.src(2) == pi | cfg.src(2) == 0) & m ~= 0)
+    A = 0;
+    return
 end
-x=cfg.kout*cfg.a;
-y=cfg.kin*cfg.a;
-Dout=cfg.Dout;
-Din=cfg.Din;
-A=-i*cfg.v*cfg.kout/Dout*spbesselh(l,1,cfg.kout*cfg.src(1))*conj(spharmonic(l,m,cfg.src(2),cfg.src(3)))...
-  *(Dout*x*spbesseljprime(l,x)*spbesselj(l,y)-Din*y*spbesselj(l,x)*spbesseljprime(l,y))...
-  /(Dout*x*spbesselhprime(l,1,x)*spbesselj(l,y)-Din*y*spbesselh(l,1,x)*spbesseljprime(l,y));
+x = cfg.kout * cfg.a;
+y = cfg.kin * cfg.a;
+Dout = cfg.Dout;
+Din = cfg.Din;
+A = -i * cfg.v * cfg.kout / Dout * spbesselh(l, 1, cfg.kout * cfg.src(1)) * conj(spharmonic(l, m, cfg.src(2), cfg.src(3))) * ...
+  (Dout * x * spbesseljprime(l, x) * spbesselj(l, y) - Din * y * spbesselj(l, x) * spbesseljprime(l, y)) / ...
+  (Dout * x * spbesselhprime(l, 1, x) * spbesselj(l, y) - Din * y * spbesselh(l, 1, x) * spbesseljprime(l, y));
diff --git a/matlab/sphdiffBcoeff.m b/matlab/sphdiffBcoeff.m
index 473b0e09..9058c785 100644
--- a/matlab/sphdiffBcoeff.m
+++ b/matlab/sphdiffBcoeff.m
@@ -1,4 +1,4 @@
-function B=sphdiffBcoeff(m,l,cfg)
+function B = sphdiffBcoeff(m, l, cfg)
 %
 % B=sphdiffBcoeff(m,l,cfg)
 %
@@ -22,4 +22,4 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-B=i*sphdiffAcoeff(m,l,cfg);
+B = i * sphdiffAcoeff(m, l, cfg);
diff --git a/matlab/sphdiffCcoeff.m b/matlab/sphdiffCcoeff.m
index c24a812d..ad082f39 100644
--- a/matlab/sphdiffCcoeff.m
+++ b/matlab/sphdiffCcoeff.m
@@ -1,4 +1,4 @@
-function C=sphdiffCcoeff(m,l,cfg)
+function C = sphdiffCcoeff(m, l, cfg)
 %
 % C=sphdiffCcoeff(m,l,cfg)
 %
@@ -22,14 +22,14 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-if((cfg.src(2)==pi | cfg.src(2)==0) & m~=0)
-    C=0;
-    return;
+if ((cfg.src(2) == pi | cfg.src(2) == 0) & m ~= 0)
+    C = 0;
+    return
 end
-x=cfg.kout*cfg.a;
-y=cfg.kin*cfg.a;
-Dout=cfg.Dout;
-Din=cfg.Din;
-C=-i*cfg.v*cfg.kout/Dout*spbesselh(l,1,cfg.kout*cfg.src(1))*conj(spharmonic(l,m,cfg.src(2),cfg.src(3)))...
-  *(Dout*x*spbesselh(l,1,x)*spbesseljprime(l,x)-Dout*x*spbesselhprime(l,1,x)*spbesselj(l,x))...
-  /(Dout*x*spbesselhprime(l,1,x)*spbesselj(l,y)-Din*y*spbesselh(l,1,x)*spbesseljprime(l,y));
+x = cfg.kout * cfg.a;
+y = cfg.kin * cfg.a;
+Dout = cfg.Dout;
+Din = cfg.Din;
+C = -i * cfg.v * cfg.kout / Dout * spbesselh(l, 1, cfg.kout * cfg.src(1)) * conj(spharmonic(l, m, cfg.src(2), cfg.src(3))) * ...
+  (Dout * x * spbesselh(l, 1, x) * spbesseljprime(l, x) - Dout * x * spbesselhprime(l, 1, x) * spbesselj(l, x)) / ...
+  (Dout * x * spbesselhprime(l, 1, x) * spbesselj(l, y) - Din * y * spbesselh(l, 1, x) * spbesseljprime(l, y));
diff --git a/matlab/sphdiffexterior.m b/matlab/sphdiffexterior.m
index b7a9883b..d0e78977 100644
--- a/matlab/sphdiffexterior.m
+++ b/matlab/sphdiffexterior.m
@@ -1,4 +1,4 @@
-function res=sphdiffexterior(r,theta,phi,cfg)
+function res = sphdiffexterior(r, theta, phi, cfg)
 %
 % res=sphdiffexterior(r,theta,phi,cfg)
 %
@@ -8,7 +8,7 @@
 %
 % input:
 %     r,theta,phi: source position in spherical coordinates.
-%     cfg: the problem domain setup: 
+%     cfg: the problem domain setup:
 %          cfg.v: speed of light in vacuum (mm/s)
 %          cfg.a: sphere radius (mm)
 %          cfg.omua: background (outside) mua (1/mm)
@@ -30,4 +30,4 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-res=sphdiffincident(r,theta,phi,cfg)+sphdiffscatter(r,theta,phi,cfg);
+res = sphdiffincident(r, theta, phi, cfg) + sphdiffscatter(r, theta, phi, cfg);
diff --git a/matlab/sphdiffincident.m b/matlab/sphdiffincident.m
index be3f0b4a..1a52ec40 100644
--- a/matlab/sphdiffincident.m
+++ b/matlab/sphdiffincident.m
@@ -1,4 +1,4 @@
-function phi=sphdiffincident(r,theta,phi,cfg)
+function phi = sphdiffincident(r, theta, phi, cfg)
 %
 % phi=sphdiffincident(r,theta,phi,cfg)
 %
@@ -8,7 +8,7 @@
 %
 % input:
 %     r,theta,phi: source position in spherical coordinates.
-%     cfg: the problem domain setup: 
+%     cfg: the problem domain setup:
 %          cfg.v: speed of light in vacuum (mm/s)
 %          cfg.a: sphere radius (mm)
 %          cfg.omua: background (outside) mua (1/mm)
@@ -31,10 +31,10 @@
 %
 
 % matlab's theta and phi are defined differently
-[xs,ys,zs] = sph2cart(cfg.src(3),pi/2-cfg.src(2),cfg.src(1));
-[x,y,z] = sph2cart(phi,pi/2-theta,r);
-dist=sqrt((x-xs).*(x-xs)+(y-ys).*(y-ys)+(z-zs).*(z-zs));
-phi=cfg.v./(4*pi*cfg.Dout*dist).*exp(i*cfg.kout*dist);
+[xs, ys, zs] = sph2cart(cfg.src(3), pi / 2 - cfg.src(2), cfg.src(1));
+[x, y, z] = sph2cart(phi, pi / 2 - theta, r);
+dist = sqrt((x - xs) .* (x - xs) + (y - ys) .* (y - ys) + (z - zs) .* (z - zs));
+phi = cfg.v ./ (4 * pi * cfg.Dout * dist) .* exp(i * cfg.kout * dist);
 
 % if(isfield(cfg,'src2'))
 %     [xs,ys,zs] = sph2cart(cfg.src2(3),pi/2-cfg.src2(2),cfg.src2(1));
diff --git a/matlab/sphdiffinterior.m b/matlab/sphdiffinterior.m
index 0825be3b..0d145505 100644
--- a/matlab/sphdiffinterior.m
+++ b/matlab/sphdiffinterior.m
@@ -1,4 +1,4 @@
-function res=sphdiffinterior(r,theta,phi,cfg)
+function res = sphdiffinterior(r, theta, phi, cfg)
 %
 % res=sphdiffinterior(r,theta,phi,cfg)
 %
@@ -8,7 +8,7 @@
 %
 % input:
 %     r,theta,phi: source position in spherical coordinates.
-%     cfg: the problem domain setup: 
+%     cfg: the problem domain setup:
 %          cfg.v: speed of light in vacuum (mm/s)
 %          cfg.a: sphere radius (mm)
 %          cfg.omua: background (outside) mua (1/mm)
@@ -30,9 +30,9 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-res=0;
-for l=0:cfg.maxl
-  for m=-l:l
-     res=res+(sphdiffCcoeff(m,l,cfg).*spbesselj(l,cfg.kin*r)).*spharmonic(l,m,theta,phi);
-  end
+res = 0;
+for l = 0:cfg.maxl
+    for m = -l:l
+        res = res + (sphdiffCcoeff(m, l, cfg) .* spbesselj(l, cfg.kin * r)) .* spharmonic(l, m, theta, phi);
+    end
 end
diff --git a/matlab/sphdiffscatter.m b/matlab/sphdiffscatter.m
index cb377031..c81a3800 100644
--- a/matlab/sphdiffscatter.m
+++ b/matlab/sphdiffscatter.m
@@ -1,14 +1,14 @@
-function res=sphdiffscatter(r,theta,phi,cfg)
+function res = sphdiffscatter(r, theta, phi, cfg)
 %
 % res=sphdiffscatter(r,theta,phi,cfg)
 %
-% sphere exterior scattered field 
+% sphere exterior scattered field
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
 %
 % input:
 %     r,theta,phi: source position in spherical coordinates.
-%     cfg: the problem domain setup: 
+%     cfg: the problem domain setup:
 %          cfg.v: speed of light in vacuum (mm/s)
 %          cfg.a: sphere radius (mm)
 %          cfg.omua: background (outside) mua (1/mm)
@@ -30,13 +30,13 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-%if(cfg.src(2)<pi/2)
+% if(cfg.src(2)<pi/2)
 %        theta=pi-theta; % mirror up-to-down
-%end
-res=zeros(size(r));
-for l=0:cfg.maxl
-  for m=-l:l
-     res=res+(sphdiffAcoeff(m,l,cfg)*spbesselj(l,cfg.kout*r)+sphdiffBcoeff(m,l,cfg)...
-        *spbessely(l,cfg.kout*r)).*spharmonic(l,m,theta,phi);
-  end
+% end
+res = zeros(size(r));
+for l = 0:cfg.maxl
+    for m = -l:l
+        res = res + (sphdiffAcoeff(m, l, cfg) * spbesselj(l, cfg.kout * r) + sphdiffBcoeff(m, l, cfg) * ...
+                     spbessely(l, cfg.kout * r)) .* spharmonic(l, m, theta, phi);
+    end
 end
diff --git a/matlab/sphdiffusion.m b/matlab/sphdiffusion.m
index ea22ccc8..1b6a24cb 100644
--- a/matlab/sphdiffusion.m
+++ b/matlab/sphdiffusion.m
@@ -1,15 +1,15 @@
-function [res,xi,yi,zi]=sphdiffusion(xrange,yrange,zrange,cfg)
+function [res, xi, yi, zi] = sphdiffusion(xrange, yrange, zrange, cfg)
 %
 % [res,xi,yi,zi]=sphdiffusion(xrange,yrange,zrange,cfg)
 %
-% diffusion solution for a sphere inside the infinite homogeneous medium 
+% diffusion solution for a sphere inside the infinite homogeneous medium
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
 %
 % input:
 %     xrange,yrange,zrange: a vector from where a grid will be created
-%       		    and the phi values will be calculated
-%     cfg: the problem domain setup: 
+%                   and the phi values will be calculated
+%     cfg: the problem domain setup:
 %          cfg.v: speed of light in vacuum (mm/s)
 %          cfg.a: sphere radius (mm)
 %          cfg.omua: background (outside) mua (1/mm)
@@ -32,64 +32,63 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-
-if(nargin<4)
-	cfg.v=299792458000;
-	cfg.a=10;
-	cfg.omua=0.002;
-	cfg.omusp=0.990;
-	cfg.imua=0.050;
-	cfg.imusp=0.500;
-	cfg.src=[30,pi,0];
-	cfg.maxl=20;
-	cfg.omega=0;
+if (nargin < 4)
+    cfg.v = 299792458000;
+    cfg.a = 10;
+    cfg.omua = 0.002;
+    cfg.omusp = 0.990;
+    cfg.imua = 0.050;
+    cfg.imusp = 0.500;
+    cfg.src = [30, pi, 0];
+    cfg.maxl = 20;
+    cfg.omega = 0;
 end
 
-cfg.Din=cfg.v/(3*cfg.imusp);
-cfg.Dout=cfg.v/(3*cfg.omusp);
-cfg.kin=sqrt((-cfg.v*cfg.imua+i*cfg.omega)/cfg.Din);
-cfg.kout=sqrt((-cfg.v*cfg.omua+i*cfg.omega)/cfg.Dout);
+cfg.Din = cfg.v / (3 * cfg.imusp);
+cfg.Dout = cfg.v / (3 * cfg.omusp);
+cfg.kin = sqrt((-cfg.v * cfg.imua + i * cfg.omega) / cfg.Din);
+cfg.kout = sqrt((-cfg.v * cfg.omua + i * cfg.omega) / cfg.Dout);
 
-[xi,yi,zi]=meshgrid(xrange,yrange,zrange);
+[xi, yi, zi] = meshgrid(xrange, yrange, zrange);
 
-[P,T,R]=cart2sph(xi(:),yi(:),zi(:)); % matlab's theta and phi are defined differently
-T=pi/2-T;
+[P, T, R] = cart2sph(xi(:), yi(:), zi(:)); % matlab's theta and phi are defined differently
+T = pi / 2 - T;
 
-idx=find(R>cfg.a);
-res=zeros(length(R),1);
-res(idx)=sphdiffexterior(R(idx),T(idx),P(idx),cfg);
+idx = find(R > cfg.a);
+res = zeros(length(R), 1);
+res(idx) = sphdiffexterior(R(idx), T(idx), P(idx), cfg);
 
-idx=find(R<=cfg.a);
-res(idx)=sphdiffinterior(R(idx),T(idx),P(idx),cfg);
+idx = find(R <= cfg.a);
+res(idx) = sphdiffinterior(R(idx), T(idx), P(idx), cfg);
 
-res=squeeze(reshape(res,size(xi)));
-xi=squeeze(xi);
-yi=squeeze(yi);
-zi=squeeze(zi);
+res = squeeze(reshape(res, size(xi)));
+xi = squeeze(xi);
+yi = squeeze(yi);
+zi = squeeze(zi);
 
-%%-------------------------------------------------------
+%% -------------------------------------------------------
 
-function res=sphdiffexterior(r,theta,phi,cfg)
-res=sphdiffincident(r,theta,phi,cfg)+sphdiffscatter(r,theta,phi,cfg);
+function res = sphdiffexterior(r, theta, phi, cfg)
+res = sphdiffincident(r, theta, phi, cfg) + sphdiffscatter(r, theta, phi, cfg);
 
-%%-------------------------------------------------------
+%% -------------------------------------------------------
 
-function res=sphdiffinterior(r,theta,phi,cfg)
-res=0;
-for l=0:cfg.maxl
-  for m=-l:l
-     res=res+(sphdiffCcoeff(m,l,cfg).*spbesselj(l,cfg.kin*r)).*spharmonic(l,m,theta,phi);
-  end
+function res = sphdiffinterior(r, theta, phi, cfg)
+res = 0;
+for l = 0:cfg.maxl
+    for m = -l:l
+        res = res + (sphdiffCcoeff(m, l, cfg) .* spbesselj(l, cfg.kin * r)) .* spharmonic(l, m, theta, phi);
+    end
 end
 
-%%-------------------------------------------------------
+%% -------------------------------------------------------
 
-function phi=sphdiffincident(r,theta,phi,cfg)
+function phi = sphdiffincident(r, theta, phi, cfg)
 % matlab's theta and phi are defined differently
-[xs,ys,zs] = sph2cart(cfg.src(3),pi/2-cfg.src(2),cfg.src(1));
-[x,y,z] = sph2cart(phi,pi/2-theta,r);
-dist=sqrt((x-xs).*(x-xs)+(y-ys).*(y-ys)+(z-zs).*(z-zs));
-phi=cfg.v./(4*pi*cfg.Dout*dist).*exp(i*cfg.kout*dist);
+[xs, ys, zs] = sph2cart(cfg.src(3), pi / 2 - cfg.src(2), cfg.src(1));
+[x, y, z] = sph2cart(phi, pi / 2 - theta, r);
+dist = sqrt((x - xs) .* (x - xs) + (y - ys) .* (y - ys) + (z - zs) .* (z - zs));
+phi = cfg.v ./ (4 * pi * cfg.Dout * dist) .* exp(i * cfg.kout * dist);
 
 % if(isfield(cfg,'src2'))
 %     [xs,ys,zs] = sph2cart(cfg.src2(3),pi/2-cfg.src2(2),cfg.src2(1));
@@ -98,116 +97,113 @@
 %     phi=phi-cfg.v./(4*pi*cfg.Dout*dist).*exp(i*cfg.kout*dist);
 % end
 
-%%-------------------------------------------------------
+%% -------------------------------------------------------
 
-function res=sphdiffscatter(r,theta,phi,cfg)
-res=zeros(size(r));
-for l=0:cfg.maxl
-  for m=-l:l
-     res=res+(sphdiffAcoeff(m,l,cfg)*spbesselj(l,cfg.kout*r)+sphdiffBcoeff(m,l,cfg)...
-        *spbessely(l,cfg.kout*r)).*spharmonic(l,m,theta,phi);
-  end
+function res = sphdiffscatter(r, theta, phi, cfg)
+res = zeros(size(r));
+for l = 0:cfg.maxl
+    for m = -l:l
+        res = res + (sphdiffAcoeff(m, l, cfg) * spbesselj(l, cfg.kout * r) + sphdiffBcoeff(m, l, cfg) * ...
+                     spbessely(l, cfg.kout * r)) .* spharmonic(l, m, theta, phi);
+    end
 end
 
-%%-------------------------------------------------------
-
-function A=sphdiffAcoeff(m,l,cfg)
-x=cfg.kout*cfg.a;
-y=cfg.kin*cfg.a;
-Dout=cfg.Dout;
-Din=cfg.Din;
-A=-i*cfg.v*cfg.kout/Dout*spbesselh(l,1,cfg.kout*cfg.src(1))*conj(spharmonic(l,m,pi,0))...
-  *(Dout*x*spbesseljprime(l,x)*spbesselj(l,y)-Din*y*spbesselj(l,x)*spbesseljprime(l,y))...
-  /(Dout*x*spbesselhprime(l,1,x)*spbesselj(l,y)-Din*y*spbesselh(l,1,x)*spbesseljprime(l,y));
-
-%%-------------------------------------------------------
-
-function B=sphdiffBcoeff(m,l,cfg)
-B=i*sphdiffAcoeff(m,l,cfg);
-
-%%-------------------------------------------------------
-
-function C=sphdiffCcoeff(m,l,cfg)
-x=cfg.kout*cfg.a;
-y=cfg.kin*cfg.a;
-Dout=cfg.Dout;
-Din=cfg.Din;
-C=-i*cfg.v*cfg.kout/Dout*spbesselh(l,1,cfg.kout*cfg.src(1))*conj(spharmonic(l,m,pi,0))...
-  *(Dout*x*spbesselh(l,1,x)*spbesseljprime(l,x)-Dout*x*spbesselhprime(l,1,x)*spbesselj(l,x))...
-  /(Dout*x*spbesselhprime(l,1,x)*spbesselj(l,y)-Din*y*spbesselh(l,1,x)*spbesseljprime(l,y));
-
-%%-------------------------------------------------------
-
-function Y=spharmonic(l,m,theta,phi)
-coeff=1;
-oldm=m;
-if(m<0)
-    coeff=(-1)^m*prod(1:(l-m))/prod(1:(l+m));
-    m=-m;
+%% -------------------------------------------------------
+
+function A = sphdiffAcoeff(m, l, cfg)
+x = cfg.kout * cfg.a;
+y = cfg.kin * cfg.a;
+Dout = cfg.Dout;
+Din = cfg.Din;
+A = -i * cfg.v * cfg.kout / Dout * spbesselh(l, 1, cfg.kout * cfg.src(1)) * conj(spharmonic(l, m, pi, 0)) * ...
+  (Dout * x * spbesseljprime(l, x) * spbesselj(l, y) - Din * y * spbesselj(l, x) * spbesseljprime(l, y)) / ...
+  (Dout * x * spbesselhprime(l, 1, x) * spbesselj(l, y) - Din * y * spbesselh(l, 1, x) * spbesseljprime(l, y));
+
+%% -------------------------------------------------------
+
+function B = sphdiffBcoeff(m, l, cfg)
+B = i * sphdiffAcoeff(m, l, cfg);
+
+%% -------------------------------------------------------
+
+function C = sphdiffCcoeff(m, l, cfg)
+x = cfg.kout * cfg.a;
+y = cfg.kin * cfg.a;
+Dout = cfg.Dout;
+Din = cfg.Din;
+C = -i * cfg.v * cfg.kout / Dout * spbesselh(l, 1, cfg.kout * cfg.src(1)) * conj(spharmonic(l, m, pi, 0)) * ...
+  (Dout * x * spbesselh(l, 1, x) * spbesseljprime(l, x) - Dout * x * spbesselhprime(l, 1, x) * spbesselj(l, x)) / ...
+  (Dout * x * spbesselhprime(l, 1, x) * spbesselj(l, y) - Din * y * spbesselh(l, 1, x) * spbesseljprime(l, y));
+
+%% -------------------------------------------------------
+
+function Y = spharmonic(l, m, theta, phi)
+coeff = 1;
+oldm = m;
+if (m < 0)
+    coeff = (-1)^m * prod(1:(l - m)) / prod(1:(l + m));
+    m = -m;
 end
-Lmn=legendre(l,cos(theta));
-if l~=0
-  Lmn=squeeze(Lmn(m+1,:))';
+Lmn = legendre(l, cos(theta));
+if l ~= 0
+    Lmn = squeeze(Lmn(m + 1, :))';
 end
-m=oldm;
-Y=coeff*sqrt((2*l+1)*prod(1:(l-m))/(prod(1:(l+m))*4*pi)) ...
-  *Lmn.*exp(i*m*phi);
+m = oldm;
+Y = coeff * sqrt((2 * l + 1) * prod(1:(l - m)) / (prod(1:(l + m)) * 4 * pi)) * ...
+  Lmn .* exp(i * m * phi);
 
-%%-------------------------------------------------------
+%% -------------------------------------------------------
 
-function jn=spbesselj(n,z)
-jn=besselj(n+1/2,z).*sqrt(pi./(2*z));
+function jn = spbesselj(n, z)
+jn = besselj(n + 1 / 2, z) .* sqrt(pi ./ (2 * z));
 
-%%-------------------------------------------------------
+%% -------------------------------------------------------
 
-function yn=spbessely(n,z)
-yn=bessely(n+1/2,z).*sqrt(pi./(2*z));
+function yn = spbessely(n, z)
+yn = bessely(n + 1 / 2, z) .* sqrt(pi ./ (2 * z));
 
-%%-------------------------------------------------------
+%% -------------------------------------------------------
 
-function hn=spbesselh(n,k,z)
-if(k==1)
-    hn=spbesselj(n,z)+i*spbessely(n,z);
-elseif(k==2)
-    hn=spbesselj(n,z)-i*spbessely(n,z);
+function hn = spbesselh(n, k, z)
+if (k == 1)
+    hn = spbesselj(n, z) + i * spbessely(n, z);
+elseif (k == 2)
+    hn = spbesselj(n, z) - i * spbessely(n, z);
 else
     error('wrong value for the second parameter');
 end
-%%-------------------------------------------------------
+%% -------------------------------------------------------
 
-function jp=besseljprime(n,z)
-jp=besselj(n-1,z)-n/z.*besselj(n,z);
+function jp = besseljprime(n, z)
+jp = besselj(n - 1, z) - n / z .* besselj(n, z);
 
-%%-------------------------------------------------------
+%% -------------------------------------------------------
 
-function yp=besselyprime(n,z)
-yp=bessely(n-1,z)-n/z.*bessely(n,z);
+function yp = besselyprime(n, z)
+yp = bessely(n - 1, z) - n / z .* bessely(n, z);
 
-%%-------------------------------------------------------
+%% -------------------------------------------------------
 
-function hp=besselhprime(n,k,z)
-hp=besselh(n-1,k,z)-n/z.*besselh(n,k,z);
+function hp = besselhprime(n, k, z)
+hp = besselh(n - 1, k, z) - n / z .* besselh(n, k, z);
 
-%%-------------------------------------------------------
+%% -------------------------------------------------------
 
-function jp=spbesseljprime(n,z)
-jp=besseljprime(n+1/2,z).*sqrt(pi/(2*z))-sqrt(pi/2)*besselj(n+1/2,z)./(2*z.*sqrt(z));
+function jp = spbesseljprime(n, z)
+jp = besseljprime(n + 1 / 2, z) .* sqrt(pi / (2 * z)) - sqrt(pi / 2) * besselj(n + 1 / 2, z) ./ (2 * z .* sqrt(z));
 
-%%-------------------------------------------------------
+%% -------------------------------------------------------
 
-function yp=spbesselyprime(n,z)
-yp=besselyprime(n+1/2,z).*sqrt(pi/(2*z))-sqrt(pi/2)*bessely(n+1/2,z)./(2*z.*sqrt(z));
+function yp = spbesselyprime(n, z)
+yp = besselyprime(n + 1 / 2, z) .* sqrt(pi / (2 * z)) - sqrt(pi / 2) * bessely(n + 1 / 2, z) ./ (2 * z .* sqrt(z));
 
-%%-------------------------------------------------------
+%% -------------------------------------------------------
 
-function hn=spbesselhprime(n,k,z)
-if(k==1)
-    hn=spbesseljprime(n,z)+i*spbesselyprime(n,z);
-elseif(k==2)
-    hn=spbesseljprime(n,z)-i*spbesselyprime(n,z);
+function hn = spbesselhprime(n, k, z)
+if (k == 1)
+    hn = spbesseljprime(n, z) + i * spbesselyprime(n, z);
+elseif (k == 2)
+    hn = spbesseljprime(n, z) - i * spbesselyprime(n, z);
 else
     error('wrong value for the second parameter');
 end
-
-
-
diff --git a/matlab/sphdiffusioninfinite.m b/matlab/sphdiffusioninfinite.m
index a7caae66..647edc84 100644
--- a/matlab/sphdiffusioninfinite.m
+++ b/matlab/sphdiffusioninfinite.m
@@ -1,15 +1,15 @@
-function [res,xi,yi,zi]=sphdiffusioninfinite(xrange,yrange,zrange,cfg)
+function [res, xi, yi, zi] = sphdiffusioninfinite(xrange, yrange, zrange, cfg)
 %
 % [res,xi,yi,zi]=sphdiffusioninfinite(xrange,yrange,zrange,cfg)
 %
-% diffusion solution for a sphere inside the infinite homogeneous medium 
+% diffusion solution for a sphere inside the infinite homogeneous medium
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
 %
 % input:
 %     xrange,yrange,zrange: a vector from where a grid will be created
-%       		    and the phi values will be calculated
-%     cfg: the problem domain setup: 
+%                   and the phi values will be calculated
+%     cfg: the problem domain setup:
 %          cfg.v: speed of light in vacuum (mm/s)
 %          cfg.a: sphere radius (mm)
 %          cfg.omua: background (outside) mua (1/mm)
@@ -32,36 +32,36 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-if(nargin<4)
-	cfg.v=299792458000;
-	cfg.a=10;
-	cfg.omua=0.002;
-	cfg.omusp=0.990;
-	cfg.imua=0.050;
-	cfg.imusp=0.500;
-	cfg.src=[30,pi,0];
-	cfg.maxl=20;
-	cfg.omega=0;
+if (nargin < 4)
+    cfg.v = 299792458000;
+    cfg.a = 10;
+    cfg.omua = 0.002;
+    cfg.omusp = 0.990;
+    cfg.imua = 0.050;
+    cfg.imusp = 0.500;
+    cfg.src = [30, pi, 0];
+    cfg.maxl = 20;
+    cfg.omega = 0;
 end
 
-cfg.Din=cfg.v/(3*cfg.imusp);
-cfg.Dout=cfg.v/(3*cfg.omusp);
-cfg.kin=sqrt((-cfg.v*cfg.imua+i*cfg.omega)/cfg.Din);
-cfg.kout=sqrt((-cfg.v*cfg.omua+i*cfg.omega)/cfg.Dout);
+cfg.Din = cfg.v / (3 * cfg.imusp);
+cfg.Dout = cfg.v / (3 * cfg.omusp);
+cfg.kin = sqrt((-cfg.v * cfg.imua + i * cfg.omega) / cfg.Din);
+cfg.kout = sqrt((-cfg.v * cfg.omua + i * cfg.omega) / cfg.Dout);
 
-[xi,yi,zi]=meshgrid(xrange,yrange,zrange);
+[xi, yi, zi] = meshgrid(xrange, yrange, zrange);
 
-[P,T,R]=cart2sph(xi(:),yi(:),zi(:)); % matlab's theta and phi are defined differently
-T=pi/2-T;
+[P, T, R] = cart2sph(xi(:), yi(:), zi(:)); % matlab's theta and phi are defined differently
+T = pi / 2 - T;
 
-idx=find(R>cfg.a);
-res=zeros(length(R),1);
-res(idx)=sphdiffexterior(R(idx),T(idx),P(idx),cfg);
+idx = find(R > cfg.a);
+res = zeros(length(R), 1);
+res(idx) = sphdiffexterior(R(idx), T(idx), P(idx), cfg);
 
-idx=find(R<=cfg.a);
-res(idx)=sphdiffinterior(R(idx),T(idx),P(idx),cfg);
+idx = find(R <= cfg.a);
+res(idx) = sphdiffinterior(R(idx), T(idx), P(idx), cfg);
 
-res=squeeze(reshape(res,size(xi)));
-xi=squeeze(xi);
-yi=squeeze(yi);
-zi=squeeze(zi);
+res = squeeze(reshape(res, size(xi)));
+xi = squeeze(xi);
+yi = squeeze(yi);
+zi = squeeze(zi);
diff --git a/matlab/sphdiffusionscatteronly.m b/matlab/sphdiffusionscatteronly.m
index 3386dd90..4e8647a7 100644
--- a/matlab/sphdiffusionscatteronly.m
+++ b/matlab/sphdiffusionscatteronly.m
@@ -1,4 +1,4 @@
-function [res,xi,yi,zi]=sphdiffusionscatteronly(xrange,yrange,zrange,cfg)
+function [res, xi, yi, zi] = sphdiffusionscatteronly(xrange, yrange, zrange, cfg)
 %
 % [res,xi,yi,zi]=sphdiffusionscatteronly(xrange,yrange,zrange,cfg)
 %
@@ -8,8 +8,8 @@
 %
 % input:
 %     xrange,yrange,zrange: a vector from where a grid will be created
-%       		    and the phi values will be calculated
-%     cfg: the problem domain setup: 
+%                   and the phi values will be calculated
+%     cfg: the problem domain setup:
 %          cfg.v: speed of light in vacuum (mm/s)
 %          cfg.a: sphere radius (mm)
 %          cfg.omua: background (outside) mua (1/mm)
@@ -32,33 +32,33 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-if(nargin<4)
-	cfg.v=299792458000;
-	cfg.a=10;
-	cfg.omua=0.002;
-	cfg.omusp=0.990;
-	cfg.imua=0.050;
-	cfg.imusp=0.500;
-	cfg.src=[30,pi,0];
-	cfg.maxl=20;
-	cfg.omega=0;
+if (nargin < 4)
+    cfg.v = 299792458000;
+    cfg.a = 10;
+    cfg.omua = 0.002;
+    cfg.omusp = 0.990;
+    cfg.imua = 0.050;
+    cfg.imusp = 0.500;
+    cfg.src = [30, pi, 0];
+    cfg.maxl = 20;
+    cfg.omega = 0;
 end
 
-cfg.Din=cfg.v/(3*cfg.imusp);
-cfg.Dout=cfg.v/(3*cfg.omusp);
-cfg.kin=sqrt((-cfg.v*cfg.imua+i*cfg.omega)/cfg.Din);
-cfg.kout=sqrt((-cfg.v*cfg.omua+i*cfg.omega)/cfg.Dout);
+cfg.Din = cfg.v / (3 * cfg.imusp);
+cfg.Dout = cfg.v / (3 * cfg.omusp);
+cfg.kin = sqrt((-cfg.v * cfg.imua + i * cfg.omega) / cfg.Din);
+cfg.kout = sqrt((-cfg.v * cfg.omua + i * cfg.omega) / cfg.Dout);
 
-[xi,yi,zi]=meshgrid(xrange,yrange,zrange);
+[xi, yi, zi] = meshgrid(xrange, yrange, zrange);
 
-[P,T,R]=cart2sph(xi(:),yi(:),zi(:)); % matlab's theta and phi are defined differently
-T=pi/2-T;
+[P, T, R] = cart2sph(xi(:), yi(:), zi(:)); % matlab's theta and phi are defined differently
+T = pi / 2 - T;
 
-idx=find(R>cfg.a);
-res=zeros(length(R),1);
-res(idx)=sphdiffscatter(R(idx),T(idx),P(idx),cfg);
+idx = find(R > cfg.a);
+res = zeros(length(R), 1);
+res(idx) = sphdiffscatter(R(idx), T(idx), P(idx), cfg);
 
-res=squeeze(reshape(res,size(xi)));
-xi=squeeze(xi);
-yi=squeeze(yi);
-zi=squeeze(zi);
+res = squeeze(reshape(res, size(xi)));
+xi = squeeze(xi);
+yi = squeeze(yi);
+zi = squeeze(zi);
diff --git a/matlab/sphdiffusionsemi.m b/matlab/sphdiffusionsemi.m
index 2978c955..90993ce1 100644
--- a/matlab/sphdiffusionsemi.m
+++ b/matlab/sphdiffusionsemi.m
@@ -1,15 +1,15 @@
-function [res,xi,yi,zi] = sphdiffusionsemi(Reff,xrange,yrange,zrange,cfg)
+function [res, xi, yi, zi] = sphdiffusionsemi(Reff, xrange, yrange, zrange, cfg)
 %
 % [res,xi,yi,zi]= sphdiffusionsemi(Reff,xrange,yrange,zrange,cfg)
 %
-% diffusion solution for a sphere inside a semi-infinite homogeneous medium 
+% diffusion solution for a sphere inside a semi-infinite homogeneous medium
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
 %
 % input:
 %     Reff:  the effective reflection coeff.
 %     xrange,yrange,zrange: a vector from where a grid will be created
-%       		    and the phi values will be calculated
+%                   and the phi values will be calculated
 %     cfg: domain structure for internal/external parameters
 %          cfg.v: speed of light in vacuum (mm/s)
 %          cfg.a: sphere radius (mm)
@@ -34,66 +34,65 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-
-if(nargin<5)
-	cfg.v=299792458000;  % mm/s
-	cfg.a=10;            % radius, mm
-	cfg.omua=0.002;      % outside mua 1/mm
-	cfg.omusp=0.990;     % outside mus' 1/mm
-	cfg.imua=0.050;
-	cfg.imusp=0.500;
-% 	cfg.imua=0.002;
-% 	cfg.imusp=0.990;
-	cfg.src=[30,pi,0];
-	cfg.maxl=20;
-	cfg.omega=0;
+if (nargin < 5)
+    cfg.v = 299792458000;  % mm/s
+    cfg.a = 10;            % radius, mm
+    cfg.omua = 0.002;      % outside mua 1/mm
+    cfg.omusp = 0.990;     % outside mus' 1/mm
+    cfg.imua = 0.050;
+    cfg.imusp = 0.500;
+    %   cfg.imua=0.002;
+    %   cfg.imusp=0.990;
+    cfg.src = [30, pi, 0];
+    cfg.maxl = 20;
+    cfg.omega = 0;
 end
-cfg.Din=cfg.v/(3*cfg.imusp);
-cfg.Dout=cfg.v/(3*cfg.omusp);
-cfg.kin=sqrt((-cfg.v*cfg.imua+i*cfg.omega)/cfg.Din);
-cfg.kout=sqrt((-cfg.v*cfg.omua+i*cfg.omega)/cfg.Dout);
-D = 1/(3*(cfg.omua+cfg.omusp));
+cfg.Din = cfg.v / (3 * cfg.imusp);
+cfg.Dout = cfg.v / (3 * cfg.omusp);
+cfg.kin = sqrt((-cfg.v * cfg.imua + i * cfg.omega) / cfg.Din);
+cfg.kout = sqrt((-cfg.v * cfg.omua + i * cfg.omega) / cfg.Dout);
+D = 1 / (3 * (cfg.omua + cfg.omusp));
 
-zb = (1+Reff)/(1-Reff)*2*D;
+zb = (1 + Reff) / (1 - Reff) * 2 * D;
 
-z0 = 1/(cfg.omusp+cfg.omua);
+z0 = 1 / (cfg.omusp + cfg.omua);
 
-src0=cfg.src;
-cfg.src(1)=src0(1)-z0;
+src0 = cfg.src;
+cfg.src(1) = src0(1) - z0;
 
 % real source full field for the real sphere
-[res,xi,yi,zi]=sphdiffusioninfinite(xrange,yrange,zrange,cfg); % S1,O1
+[res, xi, yi, zi] = sphdiffusioninfinite(xrange, yrange, zrange, cfg); % S1,O1
 
-cfg.src=src0;
-cfg.src(2)=pi;
-cfg.src(1)=src0(1)+z0+2*zb;
+cfg.src = src0;
+cfg.src(2) = pi;
+cfg.src(1) = src0(1) + z0 + 2 * zb;
 % image source full field for the real sphere
-res2=sphdiffusioninfinite(xrange,yrange,zrange,cfg); % S2,O1
+res2 = sphdiffusioninfinite(xrange, yrange, zrange, cfg); % S2,O1
 
-res=res-res2;
+res = res - res2;
 
-[P,T,R]=cart2sph(xi(:),yi(:),zi(:)); 
-T=pi/2-T;  % matlab's theta and phi are defined differently
-idx=find(R>cfg.a);
+[P, T, R] = cart2sph(xi(:), yi(:), zi(:));
+T = pi / 2 - T;  % matlab's theta and phi are defined differently
+idx = find(R > cfg.a);
 
-zrange=zrange+2*(src0(1)+zb);
+zrange = zrange + 2 * (src0(1) + zb);
 
-cfg.src=src0;
-cfg.src(2)=0;
-cfg.src(1)=src0(1)+z0+2*zb;
+cfg.src = src0;
+cfg.src(2) = 0;
+cfg.src(1) = src0(1) + z0 + 2 * zb;
 % real source scattered field for the imaged sphere outside the real sphere
-res2=sphdiffusionscatteronly(xrange,yrange,zrange,cfg); % S1,O2
+res2 = sphdiffusionscatteronly(xrange, yrange, zrange, cfg); % S1,O2
 
-res(idx)=res(idx)+res2(idx);
+res(idx) = res(idx) + res2(idx);
 
-cfg.src=src0;
-cfg.src(2)=0;
-cfg.src(1)=src0(1)-z0;
+cfg.src = src0;
+cfg.src(2) = 0;
+cfg.src(1) = src0(1) - z0;
 % image source scattered field for the imaged sphere outside the real
 % sphere
-res2=sphdiffusionscatteronly(xrange,yrange,zrange,cfg); % S2,O2
+res2 = sphdiffusionscatteronly(xrange, yrange, zrange, cfg); % S2,O2
 
-res(idx)=res(idx)-res2(idx);
+res(idx) = res(idx) - res2(idx);
 
 % high order terms are ignored, for example, the Phi(S2,O2) scattered by
 % real sphere O1, or Phi(S1,O1) scatted by the mirrored sphere O2 etc
@@ -129,4 +128,3 @@
 %                    `......'
 %
 %
-
diff --git a/matlab/sphdiffusionslab.m b/matlab/sphdiffusionslab.m
index 329ccd4f..fcdf36a3 100644
--- a/matlab/sphdiffusionslab.m
+++ b/matlab/sphdiffusionslab.m
@@ -1,15 +1,15 @@
-function [res,xi,yi,zi] = sphdiffusionslab(Reff1,Reff2,h,xrange,yrange,zrange,cfg)
+function [res, xi, yi, zi] = sphdiffusionslab(Reff1, Reff2, h, xrange, yrange, zrange, cfg)
 %
 % [res,xi,yi,zi]= sphdiffusionslab(Reff,h,xrange,yrange,zrange,cfg)
 %
-% diffusion solution for a sphere inside an infinite homogeneous slab 
+% diffusion solution for a sphere inside an infinite homogeneous slab
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
 %
 % input:
 %     Reff:  the effective reflection coeff.
 %     xrange,yrange,zrange: a vector from where a grid will be created
-%       		    and the phi values will be calculated
+%                   and the phi values will be calculated
 %     h: the height of the slab
 %     cfg: domain structure for internal/external parameters
 %          cfg.v: speed of light in vacuum (mm/s)
@@ -35,80 +35,76 @@
 % License: GPLv3, see http://mcx.sf.net/mmc/ for details
 %
 
-if(nargin<7)
-	cfg.v=299792458000;  % mm/s
-	cfg.a=10;            % radius, mm
-	cfg.omua=0.002;      % outside mua 1/mm
-	cfg.omusp=0.990;     % outside mus' 1/mm
-	cfg.imua=0.050;
-	cfg.imusp=0.500;
-% 	cfg.imua=0.002;
-% 	cfg.imusp=0.990;
-	cfg.src=[30,pi,0];
-	cfg.maxl=20;
-	cfg.omega=0;
+if (nargin < 7)
+    cfg.v = 299792458000;  % mm/s
+    cfg.a = 10;            % radius, mm
+    cfg.omua = 0.002;      % outside mua 1/mm
+    cfg.omusp = 0.990;     % outside mus' 1/mm
+    cfg.imua = 0.050;
+    cfg.imusp = 0.500;
+    %   cfg.imua=0.002;
+    %   cfg.imusp=0.990;
+    cfg.src = [30, pi, 0];
+    cfg.maxl = 20;
+    cfg.omega = 0;
 end
-cfg.Din=cfg.v/(3*cfg.imusp);
-cfg.Dout=cfg.v/(3*cfg.omusp);
-cfg.kin=sqrt((-cfg.v*cfg.imua+i*cfg.omega)/cfg.Din);
-cfg.kout=sqrt((-cfg.v*cfg.omua+i*cfg.omega)/cfg.Dout);
-src0=cfg.src;
+cfg.Din = cfg.v / (3 * cfg.imusp);
+cfg.Dout = cfg.v / (3 * cfg.omusp);
+cfg.kin = sqrt((-cfg.v * cfg.imua + i * cfg.omega) / cfg.Din);
+cfg.kout = sqrt((-cfg.v * cfg.omua + i * cfg.omega) / cfg.Dout);
+src0 = cfg.src;
 
-[res,xi,yi,zi]=sphdiffusionsemi(Reff1,xrange,yrange,zrange,cfg);
+[res, xi, yi, zi] = sphdiffusionsemi(Reff1, xrange, yrange, zrange, cfg);
 
-D = 1/(3*(cfg.omua+cfg.omusp));
-zb = (1+Reff2)/(1-Reff2)*2*D;
-z0 = 1/(cfg.omusp+cfg.omua);
+D = 1 / (3 * (cfg.omua + cfg.omusp));
+zb = (1 + Reff2) / (1 - Reff2) * 2 * D;
+z0 = 1 / (cfg.omusp + cfg.omua);
 
-cfg.src=[2*h-src0(1)+2*zb-z0, pi-src0(2), src0(3)];
+cfg.src = [2 * h - src0(1) + 2 * zb - z0, pi - src0(2), src0(3)];
 
 % image source at the upper interface full field for the real sphere
-[res2,xi,yi,zi]=sphdiffusioninfinite(xrange,yrange,zrange,cfg); % S2,O1
+[res2, xi, yi, zi] = sphdiffusioninfinite(xrange, yrange, zrange, cfg); % S2,O1
 
-res=res-res2;
+res = res - res2;
 
-cfg.src=[2*h-src0(1)+2*zb-z0+2*(z0+zb), pi-src0(2), src0(3)];
+cfg.src = [2 * h - src0(1) + 2 * zb - z0 + 2 * (z0 + zb), pi - src0(2), src0(3)];
 
 % image source at the upper interface full field for the real sphere
-[res2,xi,yi,zi]=sphdiffusioninfinite(xrange,yrange,zrange,cfg); % S2,O1
+[res2, xi, yi, zi] = sphdiffusioninfinite(xrange, yrange, zrange, cfg); % S2,O1
 
-res=res+res2;
+res = res + res2;
 
+[P, T, R] = cart2sph(xi(:), yi(:), zi(:));
+T = pi / 2 - T;  % matlab's theta and phi are defined differently
+idx = find(R > cfg.a);
 
-[P,T,R]=cart2sph(xi(:),yi(:),zi(:));
-T=pi/2-T;  % matlab's theta and phi are defined differently
-idx=find(R>cfg.a);
-
-
-cfg.src=[2*h-src0(1)-z0, src0(2), src0(3)];
+cfg.src = [2 * h - src0(1) - z0, src0(2), src0(3)];
 % real source scattered field for the imaged sphere outside the real sphere
-res2=sphdiffusionscatteronly(xrange,yrange,zrange-2*(h-src0(1)+zb),cfg); % S1,O2
+res2 = sphdiffusionscatteronly(xrange, yrange, zrange - 2 * (h - src0(1) + zb), cfg); % S1,O2
 
-res(idx)=res(idx)+res2(idx);
+res(idx) = res(idx) + res2(idx);
 
-cfg.src=[2*h-src0(1)+2*zb+z0, src0(2), src0(3)]; 
+cfg.src = [2 * h - src0(1) + 2 * zb + z0, src0(2), src0(3)];
 % image source scattered field for the imaged sphere outside the real
 % sphere
-res2=sphdiffusionscatteronly(xrange,yrange,zrange-2*(h-src0(1)+zb),cfg); % S2,O2
-
-res(idx)=res(idx)-res2(idx);
+res2 = sphdiffusionscatteronly(xrange, yrange, zrange - 2 * (h - src0(1) + zb), cfg); % S2,O2
 
+res(idx) = res(idx) - res2(idx);
 
 % this translate the grid to the origin of the mirrored sphere
 
-cfg.src=[src0(1)-z0, pi-src0(2), src0(3)];
+cfg.src = [src0(1) - z0, pi - src0(2), src0(3)];
 % real source scattered field for the imaged sphere outside the real sphere
-res2=sphdiffusionscatteronly(xrange,yrange,zrange-2*(h-src0(1)+zb),cfg); % S1,O2
+res2 = sphdiffusionscatteronly(xrange, yrange, zrange - 2 * (h - src0(1) + zb), cfg); % S1,O2
 
-res(idx)=res(idx)-res2(idx);
+res(idx) = res(idx) - res2(idx);
 
-cfg.src=[src0(1)+2*zb+z0, pi-src0(2), src0(3)];
+cfg.src = [src0(1) + 2 * zb + z0, pi - src0(2), src0(3)];
 % image source scattered field for the imaged sphere outside the real
 % sphere
-res2=sphdiffusionscatteronly(xrange,yrange,zrange-2*(h-src0(1)+zb),cfg); % S2,O2
-
-res(idx)=res(idx)+res2(idx);
+res2 = sphdiffusionscatteronly(xrange, yrange, zrange - 2 * (h - src0(1) + zb), cfg); % S2,O2
 
+res(idx) = res(idx) + res2(idx);
 
 % high order terms are ignored, for example, the Phi(S2,O2) scattered by
 % real sphere O1, or Phi(S1,O1) scatted by the mirrored sphere O2 etc
diff --git a/mmclab/example/demo_compare_mmc_mcx.m b/mmclab/example/demo_compare_mmc_mcx.m
index fc5ce3d3..64cc1341 100644
--- a/mmclab/example/demo_compare_mmc_mcx.m
+++ b/mmclab/example/demo_compare_mmc_mcx.m
@@ -1,166 +1,166 @@
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% Comparing widefield MMC and MCX in a homogeneous cubic domain
 %  (see MMC paper Fig. 2)
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %
 % In this example, we compare MMC and MCX using both simple and
 % widefield sources.
 %
 % The cubic domain has a dimension of 60x60x60 mm with optical properties
-% mua=0.001, mus=1, n=1.0 and g=0.01. The analytical solution for 
-% pencilbeam source can be computed by the cwdiffusion (for CW solution) 
+% mua=0.001, mus=1, n=1.0 and g=0.01. The analytical solution for
+% pencilbeam source can be computed by the cwdiffusion (for CW solution)
 % and tddiffusion (for time-domain solutions) functions in the
 % package of Monte Carlo eXtreme (MCX) under the mcx/utils directory.
 %
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-%addpath('/Please/add/path/to/mcx/utils/')
+% addpath('/Please/add/path/to/mcx/utils/')
 addpath('../../matlab/');
 addpath('../../mmclab/');
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% run mmclab for the 60x60x60 homogeneous cubic domain
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
 clear cfg;
 clear all;
 
-planarsrc=1; % set to 1 to compare planar src, set to 0 for pencil beam
-inclusion=1; % set to 1 to add an inclusion in the domain
+planarsrc = 1; % set to 1 to compare planar src, set to 0 for pencil beam
+inclusion = 1; % set to 1 to add an inclusion in the domain
 
-cfg.nphoton=3e7;
-cfg.seed=1648335518;
-if(~inclusion)
-    [cfg.node,tmp,cfg.elem]=meshabox([0 0 0],[60 60 60], 2*sqrt(2), 2^3/6);
-    cfg.elemprop=ones(size(cfg.elem,1),1);
-    cfg.prop=[0 0 1 1;0.005 1.0 0.01 1.0];
+cfg.nphoton = 3e7;
+cfg.seed = 1648335518;
+if (~inclusion)
+    [cfg.node, tmp, cfg.elem] = meshabox([0 0 0], [60 60 60], 2 * sqrt(2), 2^3 / 6);
+    cfg.elemprop = ones(size(cfg.elem, 1), 1);
+    cfg.prop = [0 0 1 1; 0.005 1.0 0.01 1.0];
 else
-    [node1,face1]=meshabox([0 0 0],[60 60 60], 2*sqrt(2), 2^3/6);
-    [node2,face2]=meshabox([20 20 20],[40 40 40], 2*sqrt(2), 2^3/6);
-    [node,face]=mergemesh(node1,face1,node2,face2);
-    [cfg.node,cfg.elem]=surf2mesh(node,face,[],[],1,2^3/6,[1 1 1;30 30 30],[],0);
-    cfg.elemprop=cfg.elem(:,5);
-    cfg.elem=cfg.elem(:,1:4);
-    cfg.prop=[0 0 1 1;0.005 1.0 0.01 1.0;0.01 0.2, 0.01 1.37];
+    [node1, face1] = meshabox([0 0 0], [60 60 60], 2 * sqrt(2), 2^3 / 6);
+    [node2, face2] = meshabox([20 20 20], [40 40 40], 2 * sqrt(2), 2^3 / 6);
+    [node, face] = mergemesh(node1, face1, node2, face2);
+    [cfg.node, cfg.elem] = surf2mesh(node, face, [], [], 1, 2^3 / 6, [1 1 1; 30 30 30], [], 0);
+    cfg.elemprop = cfg.elem(:, 5);
+    cfg.elem = cfg.elem(:, 1:4);
+    cfg.prop = [0 0 1 1; 0.005 1.0 0.01 1.0; 0.01 0.2, 0.01 1.37];
 end
-cfg.srcpos=[30.1,30.2,0];
+cfg.srcpos = [30.1, 30.2, 0];
 % cfg.srcdir=[0 0 1 -30]; % to test a diverging beam with a focus of -30
-cfg.srcdir=[0 0 1];
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=1e-10;
-cfg.debuglevel='TP';
-cfg.isreflect=1;
-cfg.detpos=[0 30 30 2];
-cfg.method='elem';
+cfg.srcdir = [0 0 1];
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 1e-10;
+cfg.debuglevel = 'TP';
+cfg.isreflect = 1;
+cfg.detpos = [0 30 30 2];
+cfg.method = 'elem';
 
 % define wide-field planar source
 
-if(planarsrc)   % when planar src is used, re-tessellate the mesh
-    cfg.srctype='planar';
-    cfg.srcpos=[10 10 -10];
-    cfg.srcparam1=[40 0 0 0];
-    cfg.srcparam2=[0 40 0 0];
+if (planarsrc)   % when planar src is used, re-tessellate the mesh
+    cfg.srctype = 'planar';
+    cfg.srcpos = [10 10 -10];
+    cfg.srcparam1 = [40 0 0 0];
+    cfg.srcparam2 = [0 40 0 0];
 
     % the following block before "end" can be removed as mmclab
     % has this built-in
-    srcdef=struct('srctype',cfg.srctype,'srcpos',cfg.srcpos,'srcdir',cfg.srcdir,...
-                  'srcparam1',cfg.srcparam1,'srcparam2',cfg.srcparam2);
-    if(size(cfg.elem,2)==5)
-        cfg.elem=cfg.elem(:,1:4);
+    srcdef = struct('srctype', cfg.srctype, 'srcpos', cfg.srcpos, 'srcdir', cfg.srcdir, ...
+                    'srcparam1', cfg.srcparam1, 'srcparam2', cfg.srcparam2);
+    if (size(cfg.elem, 2) == 5)
+        cfg.elem = cfg.elem(:, 1:4);
     end
-    [cfg.node,cfg.elem] = mmcaddsrc(cfg.node,[cfg.elem cfg.elemprop],...
-         mmcsrcdomain(srcdef,[min(cfg.node);max(cfg.node)]));
-    cfg.elemprop=cfg.elem(:,5);
-    cfg.elem=cfg.elem(:,1:4);
+    [cfg.node, cfg.elem] = mmcaddsrc(cfg.node, [cfg.elem cfg.elemprop], ...
+                                     mmcsrcdomain(srcdef, [min(cfg.node); max(cfg.node)]));
+    cfg.elemprop = cfg.elem(:, 5);
+    cfg.elem = cfg.elem(:, 1:4);
 end
-cfg=mmclab(cfg,'prep');
+cfg = mmclab(cfg, 'prep');
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% run mmclab
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-cube=mmclab(cfg);
-%cube=mmclab(cfg,'sse'); % this is faster
-cube=cube.data;
+cube = mmclab(cfg);
+% cube=mmclab(cfg,'sse'); % this is faster
+cube = cube.data;
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% run mcxlab for the same domain
-%%-----------------------------------------------------------------
-
-cfgx=cfg;
-cfgx=rmfield(cfgx,{'node','elem','elemprop','debuglevel','facenb','evol','e0','isreoriented'});
-dim=60;
-cfgx.vol=ones(dim,dim,dim);
-cfgx.vol=uint8(cfgx.vol);
-cfgx.faststep=0;
-if(inclusion)
-    cfgx.vol(21:40,21:40,21:40)=2;
+%% -----------------------------------------------------------------
+
+cfgx = cfg;
+cfgx = rmfield(cfgx, {'node', 'elem', 'elemprop', 'debuglevel', 'facenb', 'evol', 'e0', 'isreoriented'});
+dim = 60;
+cfgx.vol = ones(dim, dim, dim);
+cfgx.vol = uint8(cfgx.vol);
+cfgx.faststep = 0;
+if (inclusion)
+    cfgx.vol(21:40, 21:40, 21:40) = 2;
 end
-cfgx.nphoton=numel(cfgx.vol)/size(cfg.node,1)*cfg.nphoton; % for mcx, nphoton 
-                                                       % needs to be bigger 
-                                                       % to match the noise 
-                                                       % of mmc
-cfgx.autopilot=1;
-cfgx.gpuid=1;
-cfgx.issrcfrom0=1; % treating the lower-outer corner of the grid as [0 0 0]
-                   %to match mmc
-
-cubex=mcxlab(cfgx);
-cubex=cubex.data;
-
-%%-----------------------------------------------------------------
+cfgx.nphoton = numel(cfgx.vol) / size(cfg.node, 1) * cfg.nphoton; % for mcx, nphoton
+% needs to be bigger
+% to match the noise
+% of mmc
+cfgx.autopilot = 1;
+cfgx.gpuid = 1;
+cfgx.issrcfrom0 = 1; % treating the lower-outer corner of the grid as [0 0 0]
+% to match mmc
+
+cubex = mcxlab(cfgx);
+cubex = cubex.data;
+
+%% -----------------------------------------------------------------
 %% Make a cross-section
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-c0=299792458000;
+c0 = 299792458000;
 
-twin=[cfg.tstart+cfg.tstep/2:cfg.tstep:cfg.tend];
-gates=length(twin);
+twin = [cfg.tstart + cfg.tstep / 2:cfg.tstep:cfg.tend];
+gates = length(twin);
 
-cwcb=sum(cube,2);
-cwcbx=sum(cubex,4);
+cwcb = sum(cube, 2);
+cwcbx = sum(cubex, 4);
 
-[cutpos,cutvalue,facedata]=qmeshcut(cfg.elem(:,1:4),cfg.node,cwcb,'y=30.5');
-                                         % slice at y=30.5 to offset half
-                                         % grid to match mcx voxels
+[cutpos, cutvalue, facedata] = qmeshcut(cfg.elem(:, 1:4), cfg.node, cwcb, 'y=30.5');
+% slice at y=30.5 to offset half
+% grid to match mcx voxels
 
-[xi,yi]=meshgrid(0.5:59.5,0.5:59.5);     % interpolate mmc solution at 
-                                         % half-grid because mcx's voxel 
-                                         % readings are at the center of 
-                                         % the voxels
-vi=griddata(cutpos(:,1),cutpos(:,3),cutvalue,xi,yi);
-vix=squeeze(cwcbx(:,30,:))';
+[xi, yi] = meshgrid(0.5:59.5, 0.5:59.5);     % interpolate mmc solution at
+% half-grid because mcx's voxel
+% readings are at the center of
+% the voxels
+vi = griddata(cutpos(:, 1), cutpos(:, 3), cutvalue, xi, yi);
+vix = squeeze(cwcbx(:, 30, :))';
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% generate a contour plot along y=30.5
-%%-----------------------------------------------------------------
-figure
-hold on
+%% -----------------------------------------------------------------
+figure;
+hold on;
 clines = -1.5:-0.25:-8;
-if(~planarsrc && ~inclusion)
-    srcs=[30.1,30.2,0];
-    dets=[xi(:) 30.2*ones(size(xi(:))) yi(:)];
-    phicw=reshape(cwdiffusion(0.005, 1.0, 0, srcs, dets),size(xi));
-    contour(xi,yi, log10(max(squeeze(phicw),1e-8)), -1.5:-0.5:-4, 'k-' ); 
-                 % analytical is semi-infinite, only take the center part
+if (~planarsrc && ~inclusion)
+    srcs = [30.1, 30.2, 0];
+    dets = [xi(:) 30.2 * ones(size(xi(:))) yi(:)];
+    phicw = reshape(cwdiffusion(0.005, 1.0, 0, srcs, dets), size(xi));
+    contour(xi, yi, log10(max(squeeze(phicw), 1e-8)), -1.5:-0.5:-4, 'k-');
+    % analytical is semi-infinite, only take the center part
 end
-contour(xi,yi,log10(abs(vi*cfg.tstep)),clines,'r:')
-contour(xi,yi,log10(abs(vix*cfg.tstep)),clines,'b--')
+contour(xi, yi, log10(abs(vi * cfg.tstep)), clines, 'r:');
+contour(xi, yi, log10(abs(vix * cfg.tstep)), clines, 'b--');
 
-if(inclusion)
-    plot([20 20 40 40 20],[20 40 40 20 20],'k--');
+if (inclusion)
+    plot([20 20 40 40 20], [20 40 40 20 20], 'k--');
 end
 
-axis equal
-set(gca,'xlim',[1 60]);
-set(gca,'fontsize',20);
+axis equal;
+set(gca, 'xlim', [1 60]);
+set(gca, 'fontsize', 20);
 xlabel('x (mm)');
 ylabel('z (mm)');
-if(planarsrc || inclusion)
-    legend('MMC','MCX');
+if (planarsrc || inclusion)
+    legend('MMC', 'MCX');
 else
-    legend('Diffusion','MMC','MCX');
+    legend('Diffusion', 'MMC', 'MCX');
 end
 legend boxoff;
 box on;
diff --git a/mmclab/example/demo_dmmc_sphshells.m b/mmclab/example/demo_dmmc_sphshells.m
index 8163663d..35a3e167 100644
--- a/mmclab/example/demo_dmmc_sphshells.m
+++ b/mmclab/example/demo_dmmc_sphshells.m
@@ -1,178 +1,178 @@
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% validate DMMC with MMC in a heterogeneous cubic domain
 %  (see DMMC paper Fig. 1)
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %
-% In this example, we validate the DMMC algorithm with MMC using a 
+% In this example, we validate the DMMC algorithm with MMC using a
 % heterogeneous cubic domain. We also compare the DMMC/MMC solution with
 % that of voxel-based MC (MCX). This simulation generates the results
 % shown in Fig. 1(c-e) in the paper.
-% 
-%%-----------------------------------------------------------------
+%
+%% -----------------------------------------------------------------
 
 % preparation
 
-% 1. you need to add the path to iso2mesh toolbox 
+% 1. you need to add the path to iso2mesh toolbox
 % addpath('/path/to/iso2mesh/toolbox/');
 
 % 2. you need to add the path to MMC matlab folder
 % addpath('../../matlab');
 
 % create a surface mesh for a 10 mm radius sphere
-[nsph_10,fsph_10]=meshasphere([30 30 30],10,1.0);
-[nsph_10,fsph_10]=removeisolatednode(nsph_10,fsph_10);
+[nsph_10, fsph_10] = meshasphere([30 30 30], 10, 1.0);
+[nsph_10, fsph_10] = removeisolatednode(nsph_10, fsph_10);
 
 % create a surface mesh for a 23 mm radius sphere
-[nsph_23,fsph_23]=meshasphere([30 30 30],23,2.0);
-[nsph_23,fsph_23]=removeisolatednode(nsph_23,fsph_23);
+[nsph_23, fsph_23] = meshasphere([30 30 30], 23, 2.0);
+[nsph_23, fsph_23] = removeisolatednode(nsph_23, fsph_23);
 
 % create a surface mesh for a 25 mm radius sphere
-[nsph_25,fsph_25]=meshasphere([30 30 30],25,2.0);
-[nsph_25,fsph_25]=removeisolatednode(nsph_25,fsph_25);
+[nsph_25, fsph_25] = meshasphere([30 30 30], 25, 2.0);
+[nsph_25, fsph_25] = removeisolatednode(nsph_25, fsph_25);
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% create simulation parameters
-%%-----------------------------------------------------------------
-clear cfg
-
-cfg.nphoton=3e6;
-cfg.seed=1648335518;
-cfg.srcpos=[30.5,30.5,0];
-cfg.srcdir=[0 0 1];
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=5e-10;
-cfg.prop=[0,0,1,1;0.02 7.0 0.89 1.37;0.004 0.009 0.89 1.37;0.02 9.0 0.89 1.37;0.05 0.0 1.0 1.37];
-cfg.debuglevel='TP';
-cfg.isreflect=1;
-
-cfgs=[cfg cfg];
-
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
+clear cfg;
+
+cfg.nphoton = 3e6;
+cfg.seed = 1648335518;
+cfg.srcpos = [30.5, 30.5, 0];
+cfg.srcdir = [0 0 1];
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 5e-10;
+cfg.prop = [0, 0, 1, 1; 0.02 7.0 0.89 1.37; 0.004 0.009 0.89 1.37; 0.02 9.0 0.89 1.37; 0.05 0.0 1.0 1.37];
+cfg.debuglevel = 'TP';
+cfg.isreflect = 1;
+
+cfgs = [cfg cfg];
+
+%% -----------------------------------------------------------------
 %% tetrahedral mesh generation
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-% generate a coarse CDT volumetric mesh from triangular surfaces of 
+% generate a coarse CDT volumetric mesh from triangular surfaces of
 % three spheres with an additional bounding box for DMMC
 
-ISO2MESH_SESSION='dmmc1_';
+ISO2MESH_SESSION = 'dmmc1_';
 
-[nbox,ebox]=meshgrid6(0:60:60,0:60:60,0:60:60);
-fbox=volface(ebox);
-[no,fc]=mergemesh(nsph_10,fsph_10,nsph_23,fsph_23,nsph_25,fsph_25,nbox,fbox);
-[no,fc]=removeisolatednode(no,fc);
+[nbox, ebox] = meshgrid6(0:60:60, 0:60:60, 0:60:60);
+fbox = volface(ebox);
+[no, fc] = mergemesh(nsph_10, fsph_10, nsph_23, fsph_23, nsph_25, fsph_25, nbox, fbox);
+[no, fc] = removeisolatednode(no, fc);
 
-ISO2MESH_TETGENOPT='-A -q -Y'
-[cfgs(1).node,cfgs(1).elem]=surf2mesh(no,fc,[0 0 0],[60.1 60.1 60.1],1,100,[1 1 1;30 30 6;30 30 15;30 30 30]);%thin layer
+ISO2MESH_TETGENOPT = '-A -q -Y';
+[cfgs(1).node, cfgs(1).elem] = surf2mesh(no, fc, [0 0 0], [60.1 60.1 60.1], 1, 100, [1 1 1; 30 30 6; 30 30 15; 30 30 30]); % thin layer
 % [cfgs(1).node,cfgs(1).elem]=surf2mesh(no,fc,[0 0 0],[60.1 60.1 60.1],1,100,[1 1 1;30 30 6;30 30 17;30 30 30]);%thick layer
-cfgs(1).method='grid';
+cfgs(1).method = 'grid';
 
-% generate a refined volumetric mesh from triangular surfaces of 
+% generate a refined volumetric mesh from triangular surfaces of
 % three spheres with an additional bounding box for MMC
-clear ISO2MESH_TETGENOPT
-ISO2MESH_SESSION='dmmc2_';
+clear ISO2MESH_TETGENOPT;
+ISO2MESH_SESSION = 'dmmc2_';
 
-[no,fc]=mergemesh(nsph_10,fsph_10,nsph_23,fsph_23,nsph_25,fsph_25);
-[no,fc]=removeisolatednode(no,fc);
-srcpos=[30.5 30.5 0.];
-[cfgs(2).node,cfgs(2).elem,face2]=surf2mesh(no,fc,[0 0 0],[60 60 60],1,0.25,[1 1 1 0.1;30 30 6 0.1;30 30 17 0.1;30 30 30 0.1],[],[1 1 1 1 1 1 1 1]);
-[cfgs(2).node,cfgs(2).elem]=sortmesh(srcpos,cfgs(2).node,cfgs(2).elem,1:4);
-cfgs(2).method='elem';
+[no, fc] = mergemesh(nsph_10, fsph_10, nsph_23, fsph_23, nsph_25, fsph_25);
+[no, fc] = removeisolatednode(no, fc);
+srcpos = [30.5 30.5 0.];
+[cfgs(2).node, cfgs(2).elem, face2] = surf2mesh(no, fc, [0 0 0], [60 60 60], 1, 0.25, [1 1 1 0.1; 30 30 6 0.1; 30 30 17 0.1; 30 30 30 0.1], [], [1 1 1 1 1 1 1 1]);
+[cfgs(2).node, cfgs(2).elem] = sortmesh(srcpos, cfgs(2).node, cfgs(2).elem, 1:4);
+cfgs(2).method = 'elem';
 
 % % 3D view of the cross-section of the mesh: 'y>30'
 % figure;plotmesh(cfgs(1).node,cfgs(1).elem,'y>30');view(3);
 % figure;plotmesh(cfgs(2).node,cfgs(2).elem,'y>30');view(3);
 
-phimmc=mmclab(cfgs);
+phimmc = mmclab(cfgs);
 
 %% mcx
 clear cfg;
 
 % set seed to make the simulation repeatible
-cfg.seed=hex2dec('623F9A9E');
+cfg.seed = hex2dec('623F9A9E');
 
-cfg.nphoton=1e8;
+cfg.nphoton = 1e8;
 
 % define three spheres with radius=10 mm, 23 mm and 25 mm within a 60x60x60 mm box
-dim=60;
-[xi,yi,zi]=meshgrid(0.5:(dim-0.5),0.5:(dim-0.5),0.5:(dim-0.5));
-dist=(xi-30).^2+(yi-30).^2+(zi-30).^2;
-cfg.vol=ones(size(xi));
-cfg.vol(dist<625)=2;
-cfg.vol(dist<529)=3;
-cfg.vol(dist<100)=4;
-cfg.vol=uint8(cfg.vol);
+dim = 60;
+[xi, yi, zi] = meshgrid(0.5:(dim - 0.5), 0.5:(dim - 0.5), 0.5:(dim - 0.5));
+dist = (xi - 30).^2 + (yi - 30).^2 + (zi - 30).^2;
+cfg.vol = ones(size(xi));
+cfg.vol(dist < 625) = 2;
+cfg.vol(dist < 529) = 3;
+cfg.vol(dist < 100) = 4;
+cfg.vol = uint8(cfg.vol);
 
 % define the source position
-cfg.srcpos=[30.5,30.5,0];
-cfg.srcdir=[0 0 1];
-cfg.issrcfrom0=1;
+cfg.srcpos = [30.5, 30.5, 0];
+cfg.srcdir = [0 0 1];
+cfg.issrcfrom0 = 1;
 
 % format: [mua(1/mm) mus(1/mm) g n]
-cfg.prop=[0,0,1,1;0.02 7.0 0.89 1.37;0.004 0.009 0.89 1.37;0.02 9.0 0.89 1.37;0.05 0.0 1.0 1.37];
+cfg.prop = [0, 0, 1, 1; 0.02 7.0 0.89 1.37; 0.004 0.009 0.89 1.37; 0.02 9.0 0.89 1.37; 0.05 0.0 1.0 1.37];
 
 % time-domain simulation parameters
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=5e-10;
-  
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 5e-10;
+
 % GPU thread configuration
-cfg.autopilot=1;
-cfg.gpuid=1;
+cfg.autopilot = 1;
+cfg.gpuid = 1;
 
-cfg.isreflect=1; % disable reflection at exterior boundaries
-cfg.unitinmm=1; % resolution
+cfg.isreflect = 1; % disable reflection at exterior boundaries
+cfg.unitinmm = 1; % resolution
 
 %% running simulation with 1x1x1 mm input volume (60x60x60 grid)
 fprintf('running simulation ... this takes about 6 seconds on a GTX 470\n');
 tic;
-phimcx=mcxlab(cfg);
+phimcx = mcxlab(cfg);
 toc;
 
 %% data visualization
-%mcx
-phi_mcx=sum(phimcx.data,4);
-%mmc
-[xx,yy]=meshgrid(0.5:59.5,0.5:59.5);
-node1=cfgs(2).node;
-elem1=cfgs(2).elem;
-mesh0=phimmc(2).data;
-s1=sum(mesh0,2);
-[cutpos,cutvalue,facedata]=qmeshcut(elem1(:,1:4),node1,s1,[0 30.5 0; 0 30.5 1; 1 30.5 0]);
-phi_mmc=griddata(cutpos(:,1),cutpos(:,3),cutvalue,xx,yy);
-%dmmc
-phi_dmmc=sum(phimmc(1).data,4);
-phi_dmmc=phi_dmmc(1:60,1:60,1:60); 
+% mcx
+phi_mcx = sum(phimcx.data, 4);
+% mmc
+[xx, yy] = meshgrid(0.5:59.5, 0.5:59.5);
+node1 = cfgs(2).node;
+elem1 = cfgs(2).elem;
+mesh0 = phimmc(2).data;
+s1 = sum(mesh0, 2);
+[cutpos, cutvalue, facedata] = qmeshcut(elem1(:, 1:4), node1, s1, [0 30.5 0; 0 30.5 1; 1 30.5 0]);
+phi_mmc = griddata(cutpos(:, 1), cutpos(:, 3), cutvalue, xx, yy);
+% dmmc
+phi_dmmc = sum(phimmc(1).data, 4);
+phi_dmmc = phi_dmmc(1:60, 1:60, 1:60);
 
 figure;
-clines=[-10:0.5:10];
-contourf(log10(abs(squeeze(phi_mmc))),clines,'linewidth',1.5);
-hold on
-contour(log10(abs(squeeze(phi_dmmc(:,31,:))')),clines,'linestyle','--','color','w','linewidth',1.5);
-contour(log10(abs(squeeze(phi_mcx(:,31,:))')),clines,'linestyle','--','color',[0.9100    0.4100    0.1700],'linewidth',1.5);
+clines = [-10:0.5:10];
+contourf(log10(abs(squeeze(phi_mmc))), clines, 'linewidth', 1.5);
+hold on;
+contour(log10(abs(squeeze(phi_dmmc(:, 31, :))')), clines, 'linestyle', '--', 'color', 'w', 'linewidth', 1.5);
+contour(log10(abs(squeeze(phi_mcx(:, 31, :))')), clines, 'linestyle', '--', 'color', [0.9100    0.4100    0.1700], 'linewidth', 1.5);
 colorbar('EastOutside');
 
-%plot a dashed circle with radius of 10
-[xcirc,ycirc] = cylinder(10,200);
-xcirc=xcirc(1,:)+30.5;
-ycirc=ycirc(1,:)+30.5;
-plot(xcirc,ycirc,'k--','linewidth',2);
+% plot a dashed circle with radius of 10
+[xcirc, ycirc] = cylinder(10, 200);
+xcirc = xcirc(1, :) + 30.5;
+ycirc = ycirc(1, :) + 30.5;
+plot(xcirc, ycirc, 'k--', 'linewidth', 2);
 
-%plot a dashed circle with radius of 23
-[xcirc,ycirc] = cylinder(23,200);
-xcirc=xcirc(1,:)+30.5;
-ycirc=ycirc(1,:)+30.5;
-plot(xcirc,ycirc,'k--','linewidth',2);
+% plot a dashed circle with radius of 23
+[xcirc, ycirc] = cylinder(23, 200);
+xcirc = xcirc(1, :) + 30.5;
+ycirc = ycirc(1, :) + 30.5;
+plot(xcirc, ycirc, 'k--', 'linewidth', 2);
 
-%plot a dashed circle with radius of 25
-[xcirc,ycirc] = cylinder(25,200);
-xcirc=xcirc(1,:)+30.5;
-ycirc=ycirc(1,:)+30.5;
-plot(xcirc,ycirc,'k--','linewidth',2);
+% plot a dashed circle with radius of 25
+[xcirc, ycirc] = cylinder(25, 200);
+xcirc = xcirc(1, :) + 30.5;
+ycirc = ycirc(1, :) + 30.5;
+plot(xcirc, ycirc, 'k--', 'linewidth', 2);
 
 axis equal;
 colormap;
-lg=legend('MMC','DMMC','MCX','Location','northoutside','orientation','horizontal');
-set(lg,'Color',[0.5 0.5 0.5]);
-set(lg,'box','on');
-set(gca,'fontsize',18);
\ No newline at end of file
+lg = legend('MMC', 'DMMC', 'MCX', 'Location', 'northoutside', 'orientation', 'horizontal');
+set(lg, 'Color', [0.5 0.5 0.5]);
+set(lg, 'box', 'on');
+set(gca, 'fontsize', 18);
diff --git a/mmclab/example/demo_dualmesh_output.m b/mmclab/example/demo_dualmesh_output.m
index 16f1a628..c700044f 100644
--- a/mmclab/example/demo_dualmesh_output.m
+++ b/mmclab/example/demo_dualmesh_output.m
@@ -4,131 +4,131 @@
 
 % preparation
 
-% 1. you need to add the path to iso2mesh toolbox 
+% 1. you need to add the path to iso2mesh toolbox
 % addpath('/path/to/iso2mesh/toolbox/');
 
 % 2. you need to add the path to MMC matlab folder
-addpath('../../matlab')
+addpath('../../matlab');
 
 % create a surface mesh for a 10mm radius sphere
-[nsph,fsph]=meshasphere([30 30 30],10,1.0);
-[nsph,fsph]=removeisolatednode(nsph,fsph);
+[nsph, fsph] = meshasphere([30 30 30], 10, 1.0);
+[nsph, fsph] = removeisolatednode(nsph, fsph);
 
 %% create DMMC and MMC simulation parameters
-clear cfg
+clear cfg;
 
-cfg.nphoton=1e7;
-cfg.seed=1648335518;
-cfg.srcpos=[30,30.001,0];
-cfg.srcdir=[0 0 1];
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=5e-10;
-cfg.prop=[0 0 1 1;0.002 1.0 0.01 1.37;0.050 0 1 1.37];
-cfg.debuglevel='TP';
-cfg.isreflect=1;
+cfg.nphoton = 1e7;
+cfg.seed = 1648335518;
+cfg.srcpos = [30, 30.001, 0];
+cfg.srcdir = [0 0 1];
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 5e-10;
+cfg.prop = [0 0 1 1; 0.002 1.0 0.01 1.37; 0.050 0 1 1.37];
+cfg.debuglevel = 'TP';
+cfg.isreflect = 1;
 
-cfgs=[cfg cfg];
+cfgs = [cfg cfg];
 
 %% tetrahedral mesh generation
 % generate a coarse volumetric mesh from the sphere with an additional bounding box
 % the maximum element volume is 20
 
-ISO2MESH_SESSION='dmmc_';
+ISO2MESH_SESSION = 'dmmc_';
 
-[nbox,ebox]=meshgrid6(0:60:60,0:60:60,0:60:60);
-fbox=volface(ebox);
-[no,fc]=mergemesh(nbox,fbox,nsph,fsph);
+[nbox, ebox] = meshgrid6(0:60:60, 0:60:60, 0:60:60);
+fbox = volface(ebox);
+[no, fc] = mergemesh(nbox, fbox, nsph, fsph);
 
-ISO2MESH_TETGENOPT='-Y -A'
-[cfgs(1).node,cfgs(1).elem]=surf2mesh(no,fc,[0 0 0],[60.1 60.1 60.1],1,100,[1,1,1;30 30 30]);
-cfgs(1).method='grid';
+ISO2MESH_TETGENOPT = '-Y -A';
+[cfgs(1).node, cfgs(1).elem] = surf2mesh(no, fc, [0 0 0], [60.1 60.1 60.1], 1, 100, [1, 1, 1; 30 30 30]);
+cfgs(1).method = 'grid';
 
-clear ISO2MESH_TETGENOPT
-ISO2MESH_SESSION='mmc_';
+clear ISO2MESH_TETGENOPT;
+ISO2MESH_SESSION = 'mmc_';
 
-[no,el]=meshasphere([30 30 30],10,1.0);
-nodesize=[1*ones(size(no,1),1) ; 1; 1];
-srcpos=[30. 30.001 0.];
-fixednodes=[30.,30.,0.05; 30 30 30];
-nfull=[no;fixednodes];
-[cfgs(2).node,cfgs(2).elem,face2]=surf2mesh([nfull,nodesize],el,[0 0 0],[60.1 60.1 60.1],1,2,[30 30 30],[],[1 1 1 1 1 1 1 1]);
-[cfgs(2).node,cfgs(2).elem]=sortmesh(srcpos,cfgs(2).node,cfgs(2).elem,1:4);
-cfgs(2).elem(:,5)=cfgs(2).elem(:,5)+1;
-cfgs(2).method='elem';
+[no, el] = meshasphere([30 30 30], 10, 1.0);
+nodesize = [1 * ones(size(no, 1), 1); 1; 1];
+srcpos = [30. 30.001 0.];
+fixednodes = [30., 30., 0.05; 30 30 30];
+nfull = [no; fixednodes];
+[cfgs(2).node, cfgs(2).elem, face2] = surf2mesh([nfull, nodesize], el, [0 0 0], [60.1 60.1 60.1], 1, 2, [30 30 30], [], [1 1 1 1 1 1 1 1]);
+[cfgs(2).node, cfgs(2).elem] = sortmesh(srcpos, cfgs(2).node, cfgs(2).elem, 1:4);
+cfgs(2).elem(:, 5) = cfgs(2).elem(:, 5) + 1;
+cfgs(2).method = 'elem';
 
 %% running simulation with 1x1x1 mm input volume (60x60x60 grid)
-phimmc=mmclab(cfgs);
+phimmc = mmclab(cfgs);
 
 %% create MCX simulation parameters
 clear cfg;
 
 % set seed to make the simulation repeatible
-cfg.seed=hex2dec('623F9A9E');
+cfg.seed = hex2dec('623F9A9E');
 
-cfg.nphoton=3e7;
+cfg.nphoton = 3e7;
 
 % define a 1cm radius sphere within a 6x6x6 cm box
-dim=60;
-[xi,yi,zi]=meshgrid(0.5:dim-0.5,0.5:dim-0.5,0.5:dim-0.5);
-dist=(xi-30).^2+(yi-30).^2+(zi-30).^2;
-cfg.vol=ones(size(xi));
-cfg.vol(dist<100)=2;
-cfg.vol=uint8(cfg.vol);
+dim = 60;
+[xi, yi, zi] = meshgrid(0.5:dim - 0.5, 0.5:dim - 0.5, 0.5:dim - 0.5);
+dist = (xi - 30).^2 + (yi - 30).^2 + (zi - 30).^2;
+cfg.vol = ones(size(xi));
+cfg.vol(dist < 100) = 2;
+cfg.vol = uint8(cfg.vol);
 
 % define the source position, same as DMMC/MMC
-cfg.srcpos=[30,30.001,0];
-cfg.srcdir=[0 0 1];
-cfg.issrcfrom0=1;
+cfg.srcpos = [30, 30.001, 0];
+cfg.srcdir = [0 0 1];
+cfg.issrcfrom0 = 1;
 
 % format: [mua(1/mm) mus(1/mm) g n]
-cfg.prop=[0 0 1 1;0.002 1.0 0.01 1.37;0.050 0 1 1.37];
+cfg.prop = [0 0 1 1; 0.002 1.0 0.01 1.37; 0.050 0 1 1.37];
 
 % time-domain simulation parameters
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=5e-10;
-  
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 5e-10;
+
 % GPU thread configuration
-cfg.autopilot=1;
-cfg.gpuid=1;
+cfg.autopilot = 1;
+cfg.gpuid = 1;
 
 % enable reflection at exterior boundaries, same as DMMC/MMC
-cfg.isreflect=1; 
+cfg.isreflect = 1;
 
 %% running simulation with 1x1x1 mm input volume (60x60x60 grid)
 fprintf('running MCX simulation ... this takes about 6 seconds on a GTX 470\n');
 tic;
-phimcx=mcxlab(cfg);
+phimcx = mcxlab(cfg);
 toc;
 
 %% visualization: compare CW fluence maps produced by DMMC/MMC against that by MCX using contour lines
-clines=-7:0.25:-1;
-[xx,zz]=meshgrid(0.5:59.5,0.5:59.5);
-node2=cfgs(2).node;
-elem2=cfgs(2).elem;
-flux_mmc=phimmc(2).data;
-CWfluence_mmc=sum(flux_mmc,2)*cfg.tstep;
-[cutpos,cutvalue,facedata]=qmeshcut(elem2(:,1:4),node2,CWfluence_mmc,[0 30.5 0; 0 30.5 1; 1 30.5 0]);
-
-CWfluence_mmc_grid=griddata(cutpos(:,1),cutpos(:,3),cutvalue,xx,zz);
-CWfluence_dmmc=sum(phimmc(1).data,4)*cfg.tstep;
-CWfluence_mcx=sum(phimcx.data,4)*cfg.tstep;
+clines = -7:0.25:-1;
+[xx, zz] = meshgrid(0.5:59.5, 0.5:59.5);
+node2 = cfgs(2).node;
+elem2 = cfgs(2).elem;
+flux_mmc = phimmc(2).data;
+CWfluence_mmc = sum(flux_mmc, 2) * cfg.tstep;
+[cutpos, cutvalue, facedata] = qmeshcut(elem2(:, 1:4), node2, CWfluence_mmc, [0 30.5 0; 0 30.5 1; 1 30.5 0]);
+
+CWfluence_mmc_grid = griddata(cutpos(:, 1), cutpos(:, 3), cutvalue, xx, zz);
+CWfluence_dmmc = sum(phimmc(1).data, 4) * cfg.tstep;
+CWfluence_mcx = sum(phimcx.data, 4) * cfg.tstep;
 
 figure;
-contourf(xx,zz,log10(abs(squeeze(CWfluence_mmc_grid))),clines);
-hold on
-contour(xx,zz,log10(abs(squeeze(CWfluence_dmmc(1:end-1,31,1:end-1))')),clines,'linestyle','--','color','w','linewidth',1.5);
-contour(xx,zz,log10(abs(squeeze(CWfluence_mcx(:,31,:))')),clines,'linestyle','--','color',[0.9100    0.4100    0.1700],'linewidth',1.5);
+contourf(xx, zz, log10(abs(squeeze(CWfluence_mmc_grid))), clines);
+hold on;
+contour(xx, zz, log10(abs(squeeze(CWfluence_dmmc(1:end - 1, 31, 1:end - 1))')), clines, 'linestyle', '--', 'color', 'w', 'linewidth', 1.5);
+contour(xx, zz, log10(abs(squeeze(CWfluence_mcx(:, 31, :))')), clines, 'linestyle', '--', 'color', [0.9100    0.4100    0.1700], 'linewidth', 1.5);
 
-[xcirc,ycirc] = cylinder(10,200);
-xcirc=xcirc(1,:)+30;
-ycirc=ycirc(1,:)+30;
-plot(xcirc,ycirc,'k--','linewidth',2);
+[xcirc, ycirc] = cylinder(10, 200);
+xcirc = xcirc(1, :) + 30;
+ycirc = ycirc(1, :) + 30;
+plot(xcirc, ycirc, 'k--', 'linewidth', 2);
 
 axis equal;
 colormap;
-set(gca,'fontsize',20);
-lg=legend('MMC','DMMC','MCX');
-set(lg,'color','none');
-set(lg,'box','off');
+set(gca, 'fontsize', 20);
+lg = legend('MMC', 'DMMC', 'MCX');
+set(lg, 'color', 'none');
+set(lg, 'box', 'off');
diff --git a/mmclab/example/demo_example_meshtest.m b/mmclab/example/demo_example_meshtest.m
index 62bb6897..043247e8 100644
--- a/mmclab/example/demo_example_meshtest.m
+++ b/mmclab/example/demo_example_meshtest.m
@@ -4,7 +4,7 @@
 % In this example, we validate MMCM algorithm using a sphere object
 % in a homogeneous cubic background. This simulation generates the results
 % shown in Fig. 3 in the paper.
-% 
+%
 % The cubic domain has a dimension of 60x60x60 mm with optical properties
 % mua=0.002, mus=1, n=1.37 and g=0.01. A sphere is centered at [30 30 30]mm
 % with a radius of 10mm. The optical properties of the sphere is
@@ -13,7 +13,7 @@
 % sphdiffusionslab function in mmc/matlab/ directory (this has already
 % been done, the result for plane y=30 is saved in the
 % sphdiffsemiinf.mat file).
-% 
+%
 % To validate MMCM, we generate an FE-mesh for the sphere and the cube.
 % Three meshes are tested: mesh0: a coarse FE mesh with only 10,000 nodes,
 % mesh1: a uniform dense FE mesh with 60000 nodes, and mesh2: a mesh
@@ -24,212 +24,210 @@
 
 % preparation
 
-% 1. you need to add the path to iso2mesh toolbox 
+% 1. you need to add the path to iso2mesh toolbox
 % addpath('/path/to/iso2mesh/toolbox/');
 
 % 2. you need to add the path to MMC matlab folder
-addpath('../../matlab')
-
+addpath('../../matlab');
 
 % create a surface mesh for a 10mm radius sphere
-[no,el]=meshasphere([30 30 30],10,1.0);
+[no, el] = meshasphere([30 30 30], 10, 1.0);
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% create the common parameters for all 3 simulations
-%%-----------------------------------------------------------------
-clear cfg
-
-cfg.nphoton=3e7;
-cfg.seed=1648335518;
-cfg.srcpos=[30.,30.,0];
-cfg.srcdir=[0 0 1];
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=1e-10;
-cfg.prop=[0 0 1 1;0.002 1.0 0.01 1.37;0.050 5.0 0.9 1.37];
-cfg.debuglevel='TP';
-cfg.isreflect=0;
-cfg.method='elem';
-
-cfg=[cfg cfg cfg];
-
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
+clear cfg;
+
+cfg.nphoton = 3e7;
+cfg.seed = 1648335518;
+cfg.srcpos = [30., 30., 0];
+cfg.srcdir = [0 0 1];
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 1e-10;
+cfg.prop = [0 0 1 1; 0.002 1.0 0.01 1.37; 0.050 5.0 0.9 1.37];
+cfg.debuglevel = 'TP';
+cfg.isreflect = 0;
+cfg.method = 'elem';
+
+cfg = [cfg cfg cfg];
+
+%% -----------------------------------------------------------------
 %% tetrahedral mesh generation
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
 % generate a coarse volumetric mesh from the sphere with an additional bounding box
 % the maximum element volume is 20
 
-ISO2MESH_SESSION='mmcmesh2_';
+ISO2MESH_SESSION = 'mmcmesh2_';
 
-srcpos=[30. 30. 0.];
-fixednodes=[30.,30.,0.05; 30 30 30];
-nodesize=[ones(size(no,1),1) ; 0.5; 3];
-nfull=[no;fixednodes];
-[cfg(3).node,cfg(3).elem,face3]=surf2mesh([nfull,nodesize],el,[0 0 0],[60.1 60.1 60.1],1,8,[30 30 30],[],[1.5 1.5 1.5 1.5 5 5 5 5]);
-[cfg(3).node,cfg(3).elem]=sortmesh(srcpos,cfg(3).node,cfg(3).elem,1:4);
-cfg(3).elem(:,5)=cfg(3).elem(:,5)+1;
+srcpos = [30. 30. 0.];
+fixednodes = [30., 30., 0.05; 30 30 30];
+nodesize = [ones(size(no, 1), 1); 0.5; 3];
+nfull = [no; fixednodes];
+[cfg(3).node, cfg(3).elem, face3] = surf2mesh([nfull, nodesize], el, [0 0 0], [60.1 60.1 60.1], 1, 8, [30 30 30], [], [1.5 1.5 1.5 1.5 5 5 5 5]);
+[cfg(3).node, cfg(3).elem] = sortmesh(srcpos, cfg(3).node, cfg(3).elem, 1:4);
+cfg(3).elem(:, 5) = cfg(3).elem(:, 5) + 1;
 
 % generate a dense volumetric mesh from the sphere with an additional bounding box
 % the maximum element volume is 5
 
-ISO2MESH_SESSION='mmcmesh1_';
+ISO2MESH_SESSION = 'mmcmesh1_';
 
-nodesize=[1*ones(size(no,1),1) ; 1; 1];
-[cfg(2).node,cfg(2).elem,face2]=surf2mesh([nfull,nodesize],el,[0 0 0],[60.1 60.1 60.1],1,2,[30 30 30],[],[1 1 1 1 1 1 1 1]);
-[cfg(2).node,cfg(2).elem]=sortmesh(srcpos,cfg(2).node,cfg(2).elem,1:4);
-cfg(2).elem(:,5)=cfg(2).elem(:,5)+1;
+nodesize = [1 * ones(size(no, 1), 1); 1; 1];
+[cfg(2).node, cfg(2).elem, face2] = surf2mesh([nfull, nodesize], el, [0 0 0], [60.1 60.1 60.1], 1, 2, [30 30 30], [], [1 1 1 1 1 1 1 1]);
+[cfg(2).node, cfg(2).elem] = sortmesh(srcpos, cfg(2).node, cfg(2).elem, 1:4);
+cfg(2).elem(:, 5) = cfg(2).elem(:, 5) + 1;
 
 % reduce the surface node numbers to 20%
 
-ISO2MESH_SESSION='mmcmesh0_';
+ISO2MESH_SESSION = 'mmcmesh0_';
 
 % using the coarse spherical surface, we generate a coarse volumetric
 % mesh with maximum volume of 10
 
-nodesize=[ones(size(no,1),1); 3];
-nfull=[no; 30 30 30];
-[cfg(1).node,cfg(1).elem,face1]=surf2mesh([nfull,nodesize],el,[0 0 0],[60.1 60.1 60.1],1,10,[30 30 30],[],[2 2 2 2 5 5 5 5]);
-[cfg(1).node,cfg(1).elem]=sortmesh(srcpos,cfg(1).node,cfg(1).elem,1:4);
-cfg(1).elem(:,5)=cfg(1).elem(:,5)+1;
-
-clear ISO2MESH_SESSION
+nodesize = [ones(size(no, 1), 1); 3];
+nfull = [no; 30 30 30];
+[cfg(1).node, cfg(1).elem, face1] = surf2mesh([nfull, nodesize], el, [0 0 0], [60.1 60.1 60.1], 1, 10, [30 30 30], [], [2 2 2 2 5 5 5 5]);
+[cfg(1).node, cfg(1).elem] = sortmesh(srcpos, cfg(1).node, cfg(1).elem, 1:4);
+cfg(1).elem(:, 5) = cfg(1).elem(:, 5) + 1;
 
+clear ISO2MESH_SESSION;
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% running MMC simulations for all 3 cases
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-flux=mmclab(cfg);
+flux = mmclab(cfg);
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% plotting the results
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-c0=299792458000;
+c0 = 299792458000;
 
-twin=[cfg(1).tstart+cfg(1).tstep/2:cfg(1).tstep:cfg(1).tend];
-gates=length(twin);
-clines=[-1:0.5:8]-10;
+twin = [cfg(1).tstart + cfg(1).tstep / 2:cfg(1).tstep:cfg(1).tend];
+gates = length(twin);
+clines = [-1:0.5:8] - 10;
 
-[xi,yi]=meshgrid(1:60,0:60);
+[xi, yi] = meshgrid(1:60, 0:60);
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% generate/load analytical solution for sphere inside infinite slab
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-%[phi_ana,xa,ya,za]=sphdiffusionslab(0,0,60,-22:0.8:22,0,-30:0.8:10);
-%save sphdiffsemiinf.mat phi_ana xa ya za
+% [phi_ana,xa,ya,za]=sphdiffusionslab(0,0,60,-22:0.8:22,0,-30:0.8:10);
+% save sphdiffsemiinf.mat phi_ana xa ya za
 
-load ../../examples/meshtest/sphdiffsemiinf.mat
-idx=find((xa(:)<-12 | xa(:)>12) & za(:)>-5);
-phi_ana(idx)=nan;
-idx=find((xa(:)<-10 | xa(:)>10) & za(:)>0);
-phi_ana(idx)=nan;
+load ../../examples/meshtest/sphdiffsemiinf.mat;
+idx = find((xa(:) < -12 | xa(:) > 12) & za(:) > -5);
+phi_ana(idx) = nan;
+idx = find((xa(:) < -10 | xa(:) > 10) & za(:) > 0);
+phi_ana(idx) = nan;
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% generate the contour of the inclusion
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-[xcirc,ycirc] = cylinder(10,200);
-xcirc=xcirc(1,:)+30;
-ycirc=ycirc(1,:)+30;
+[xcirc, ycirc] = cylinder(10, 200);
+xcirc = xcirc(1, :) + 30;
+ycirc = ycirc(1, :) + 30;
 
 % create the voxel-contour of the sphere for MCX
-%dim=60;
-%[xv,yv,zv]=meshgrid(1:dim,1:dim,1:dim);
-%dist=(xv-30).^2+(yv-30).^2+(zv-30).^2;
+% dim=60;
+% [xv,yv,zv]=meshgrid(1:dim,1:dim,1:dim);
+% dist=(xv-30).^2+(yv-30).^2+(zv-30).^2;
 
-%vv=zeros(size(xv));
-%vv(dist<100)=1;
+% vv=zeros(size(xv));
+% vv(dist<100)=1;
 
-%c=contourc(squeeze(vv(:,30,:)),1);
-%plot(c(1,2:end),c(2,2:end),'c--')
+% c=contourc(squeeze(vv(:,30,:)),1);
+% plot(c(1,2:end),c(2,2:end),'c--')
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% plot sphere 1
-%%-----------------------------------------------------------------
-node1=cfg(1).node;
-elem1=cfg(1).elem;
-mesh0=flux(1).data;
-s1=sum(mesh0,2)*cfg(1).tstep;
-[cutpos,cutvalue,facedata]=qmeshcut(elem1(:,1:4),node1,s1,[0 30 0; 0 30 1; 1 30 0]);
-%patch('Vertices',cutpos,'Faces',facedata,'FaceVertexCData',log10(cutvalue),'FaceColor','interp','linestyle','none');
-%view([0 1 0])
-
-vi=griddata(cutpos(:,1),cutpos(:,3),cutvalue,xi,yi);
-
-figure
-hold on
-[cc,hc]=contour(xa+30,za+31,log10(abs(phi_ana)),clines,'color',[0.7 0.7 0.7],'linewidth',2);
-contour(log10(abs(vi)),clines,'r:')
-plot(xcirc,ycirc,'k--','linewidth',2);
-
-axis equal
-set(gca,'xlim',[1 60]);
-set(gca,'ylim',[1 60]);
-set(gca,'fontsize',18)
-xlabel('x (mm)')
-ylabel('z (mm)')
-legend('Diffusion','MMCM')
+%% -----------------------------------------------------------------
+node1 = cfg(1).node;
+elem1 = cfg(1).elem;
+mesh0 = flux(1).data;
+s1 = sum(mesh0, 2) * cfg(1).tstep;
+[cutpos, cutvalue, facedata] = qmeshcut(elem1(:, 1:4), node1, s1, [0 30 0; 0 30 1; 1 30 0]);
+% patch('Vertices',cutpos,'Faces',facedata,'FaceVertexCData',log10(cutvalue),'FaceColor','interp','linestyle','none');
+% view([0 1 0])
+
+vi = griddata(cutpos(:, 1), cutpos(:, 3), cutvalue, xi, yi);
+
+figure;
+hold on;
+[cc, hc] = contour(xa + 30, za + 31, log10(abs(phi_ana)), clines, 'color', [0.7 0.7 0.7], 'linewidth', 2);
+contour(log10(abs(vi)), clines, 'r:');
+plot(xcirc, ycirc, 'k--', 'linewidth', 2);
+
+axis equal;
+set(gca, 'xlim', [1 60]);
+set(gca, 'ylim', [1 60]);
+set(gca, 'fontsize', 18);
+xlabel('x (mm)');
+ylabel('z (mm)');
+legend('Diffusion', 'MMCM');
 legend boxoff;
 box on;
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% plot sphere 2
-%%-----------------------------------------------------------------
-
-node2=cfg(2).node;
-elem2=cfg(2).elem;
-mesh1=flux(2).data;
-s2=sum(mesh1,2)*cfg(1).tstep;
-[cutpos,cutvalue,facedata]=qmeshcut(elem2(:,1:4),node2,s2,[0 30 0; 0 30 1; 1 30 0]);
-%patch('Vertices',cutpos,'Faces',facedata,'FaceVertexCData',log10(cutvalue),'FaceColor','interp','linestyle','none');
-%view([0 1 0])
-vi=griddata(cutpos(:,1),cutpos(:,3),cutvalue,xi,yi);
-
-figure
-hold on
-[cc,hc]=contour(xa+30,za+31,log10(abs(phi_ana)),clines,'color',[0.7 0.7 0.7],'linewidth',2);
-contour(log10(abs(vi)),clines,'r:')
-plot(xcirc,ycirc,'k--','linewidth',2);
-
-axis equal
-set(gca,'xlim',[1 60]);
-set(gca,'ylim',[1 60]);
-set(gca,'fontsize',18)
-xlabel('x (mm)')
-ylabel('z (mm)')
-legend('Diffusion','MMCM')
+%% -----------------------------------------------------------------
+
+node2 = cfg(2).node;
+elem2 = cfg(2).elem;
+mesh1 = flux(2).data;
+s2 = sum(mesh1, 2) * cfg(1).tstep;
+[cutpos, cutvalue, facedata] = qmeshcut(elem2(:, 1:4), node2, s2, [0 30 0; 0 30 1; 1 30 0]);
+% patch('Vertices',cutpos,'Faces',facedata,'FaceVertexCData',log10(cutvalue),'FaceColor','interp','linestyle','none');
+% view([0 1 0])
+vi = griddata(cutpos(:, 1), cutpos(:, 3), cutvalue, xi, yi);
+
+figure;
+hold on;
+[cc, hc] = contour(xa + 30, za + 31, log10(abs(phi_ana)), clines, 'color', [0.7 0.7 0.7], 'linewidth', 2);
+contour(log10(abs(vi)), clines, 'r:');
+plot(xcirc, ycirc, 'k--', 'linewidth', 2);
+
+axis equal;
+set(gca, 'xlim', [1 60]);
+set(gca, 'ylim', [1 60]);
+set(gca, 'fontsize', 18);
+xlabel('x (mm)');
+ylabel('z (mm)');
+legend('Diffusion', 'MMCM');
 legend boxoff;
 box on;
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% plot sphere 3
-%%-----------------------------------------------------------------
-
-node3=cfg(3).node;
-elem3=cfg(3).elem;
-mesh2=flux(3).data;
-s3=sum(mesh2,2)*cfg(1).tstep;
-[cutpos,cutvalue,facedata]=qmeshcut(elem3(:,1:4),node3,s3,[0 29 0; 0 29 1; 1 29 0]);
-
-vi=griddata(cutpos(:,1),cutpos(:,3),cutvalue,xi,yi);
-
-figure
-%patch('Vertices',cutpos,'Faces',facedata,'FaceVertexCData',log10(cutvalue),'FaceColor','interp','linestyle','none');
-%view([0 1 0])
-hold on
-[cc,hc]=contour(xa+30,za+31,log10(abs(phi_ana)),clines,'color',[0.7 0.7 0.7],'linewidth',2);
-contour(log10(abs(vi)),clines,'r:')
-plot(xcirc,ycirc,'k--','linewidth',2);
-
-axis equal
-set(gca,'xlim',[1 60]);
-set(gca,'ylim',[1 60]);
-set(gca,'fontsize',18)
-xlabel('x (mm)')
-ylabel('z (mm)')
-legend('Diffusion','MMCM')
+%% -----------------------------------------------------------------
+
+node3 = cfg(3).node;
+elem3 = cfg(3).elem;
+mesh2 = flux(3).data;
+s3 = sum(mesh2, 2) * cfg(1).tstep;
+[cutpos, cutvalue, facedata] = qmeshcut(elem3(:, 1:4), node3, s3, [0 29 0; 0 29 1; 1 29 0]);
+
+vi = griddata(cutpos(:, 1), cutpos(:, 3), cutvalue, xi, yi);
+
+figure;
+% patch('Vertices',cutpos,'Faces',facedata,'FaceVertexCData',log10(cutvalue),'FaceColor','interp','linestyle','none');
+% view([0 1 0])
+hold on;
+[cc, hc] = contour(xa + 30, za + 31, log10(abs(phi_ana)), clines, 'color', [0.7 0.7 0.7], 'linewidth', 2);
+contour(log10(abs(vi)), clines, 'r:');
+plot(xcirc, ycirc, 'k--', 'linewidth', 2);
+
+axis equal;
+set(gca, 'xlim', [1 60]);
+set(gca, 'ylim', [1 60]);
+set(gca, 'fontsize', 18);
+xlabel('x (mm)');
+ylabel('z (mm)');
+legend('Diffusion', 'MMCM');
 legend boxoff;
 box on;
diff --git a/mmclab/example/demo_example_onecube.m b/mmclab/example/demo_example_onecube.m
index 61ef6199..3c03d652 100644
--- a/mmclab/example/demo_example_onecube.m
+++ b/mmclab/example/demo_example_onecube.m
@@ -1,6 +1,6 @@
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% simple demonstration for debug flags
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %
 % In this example, we run photon migration in a toy-problem to show
 % the basic steps and behaviors of the simulation code.
@@ -13,34 +13,32 @@
 % accumulation sites. Using a matlab script, one can visualize
 % the photon moving from the output of the simulation.
 %
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% defining mesh and input structure
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
 addpath('../../matlab/');
 
-[cfg.node,cfg.elem]=genT6mesh(0:10:10,0:10:10,0:10:10);
-cfg.elem=sortrows(cfg.elem);
-cfg.elemprop=ones(size(cfg.elem,1),1);
-cfg.prop=[0 0 1 1;0.005 1.0101010101 0.01 1.0];
-cfg.srcpos=[2,8,0];
-cfg.srcdir=[0 0 1];
-cfg.seed=1648335518;
-cfg.nphoton=100;
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=5e-10;
-
-%%-----------------------------------------------------------------
+[cfg.node, cfg.elem] = genT6mesh(0:10:10, 0:10:10, 0:10:10);
+cfg.elem = sortrows(cfg.elem);
+cfg.elemprop = ones(size(cfg.elem, 1), 1);
+cfg.prop = [0 0 1 1; 0.005 1.0101010101 0.01 1.0];
+cfg.srcpos = [2, 8, 0];
+cfg.srcdir = [0 0 1];
+cfg.seed = 1648335518;
+cfg.nphoton = 100;
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 5e-10;
+
+%% -----------------------------------------------------------------
 %% run simulation and print out photon movement
-%%-----------------------------------------------------------------
-
-cfg.debuglevel='M';
-flux=mmclab(cfg);
-
-cfg.debuglevel='A';
-flux=mmclab(cfg);
+%% -----------------------------------------------------------------
 
+cfg.debuglevel = 'M';
+flux = mmclab(cfg);
 
+cfg.debuglevel = 'A';
+flux = mmclab(cfg);
diff --git a/mmclab/example/demo_example_replay.m b/mmclab/example/demo_example_replay.m
index ae5ea4ef..e7ef49db 100644
--- a/mmclab/example/demo_example_replay.m
+++ b/mmclab/example/demo_example_replay.m
@@ -1,104 +1,104 @@
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% demonstration of the replay feature
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %
 % In this example, we run MMC using a homogeneous cubic domain,
 % same as in demo_example_validation.m. We save the seeds of the
-% detected photons, and then rerun these photons again (i.e. 
+% detected photons, and then rerun these photons again (i.e.
 % the "replay" part). This feature allows one to identify features
 % that are only related to a source/detector pair.
 %
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
 addpath('../../matlab/');
 
 % define 1 source and 4 detectors for a uniform cube
 
-clear cfg newcfg
-
-cfg.nphoton=1e6;
-cfg.seed=1648335518;
-[cfg.node,cfg.elem]=genT6mesh(0:2:60,0:2:60,0:2:60);
-cfg.elemprop=ones(size(cfg.elem,1),1);
-cfg.srcpos=[30.1,30.2,0];
-cfg.srcdir=[0 0 1];
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=5e-9;
-cfg.prop=[0 0 1 1;0.005 1.0 0.01 1.0];
-cfg.debuglevel='TP';
-cfg.method='elem';
-cfg.isreflect=0;
-cfg.detpos=[30. 20. 0. 1.
-   30. 40. 0. 1.
-   20. 30. 0. 1.
-   40. 30. 0. 1.];
-cfg.issaveexit=1;  % save detected photon exit position and angles
-cfg.issaveseed=1;  % save detected photon seeds to replay later
+clear cfg newcfg;
+
+cfg.nphoton = 1e6;
+cfg.seed = 1648335518;
+[cfg.node, cfg.elem] = genT6mesh(0:2:60, 0:2:60, 0:2:60);
+cfg.elemprop = ones(size(cfg.elem, 1), 1);
+cfg.srcpos = [30.1, 30.2, 0];
+cfg.srcdir = [0 0 1];
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 5e-9;
+cfg.prop = [0 0 1 1; 0.005 1.0 0.01 1.0];
+cfg.debuglevel = 'TP';
+cfg.method = 'elem';
+cfg.isreflect = 0;
+cfg.detpos = [30. 20. 0. 1.
+              30. 40. 0. 1.
+              20. 30. 0. 1.
+              40. 30. 0. 1.];
+cfg.issaveexit = 1;  % save detected photon exit position and angles
+cfg.issaveseed = 1;  % save detected photon seeds to replay later
 % cfg.method=0;
 
-newcfg=mmclab(cfg,'prep');  % preprocessing of the mesh to get the missing fields
+newcfg = mmclab(cfg, 'prep');  % preprocessing of the mesh to get the missing fields
 
-[cube, detp, ncfg, seeds]=mmclab(newcfg); % initial simulation
+[cube, detp, ncfg, seeds] = mmclab(newcfg); % initial simulation
 
 % set up for wl replay
 
-newcfg.replaydet=1;     % replay photons detected by det#1
-newcfg.seed=seeds.data(:,detp.data(1,:)==newcfg.replaydet);
-detp.ppath=detp.ppath(detp.data(1,:)==newcfg.replaydet,:);
-detp.w0=detp.w0(detp.data(1,:)==newcfg.replaydet,:);
-detp.data=detp.data(:,detp.data(1,:)==newcfg.replaydet);
+newcfg.replaydet = 1;     % replay photons detected by det#1
+newcfg.seed = seeds.data(:, detp.data(1, :) == newcfg.replaydet);
+detp.ppath = detp.ppath(detp.data(1, :) == newcfg.replaydet, :);
+detp.w0 = detp.w0(detp.data(1, :) == newcfg.replaydet, :);
+detp.data = detp.data(:, detp.data(1, :) == newcfg.replaydet);
 % calculate the detected photon weight using the partial path output and prop
-newcfg.replayweight=mmcdetweight(detp,newcfg.prop);
-newcfg.replaytime=mmcdettime(detp,newcfg.prop);
-newcfg.isnormalized=0;
-newcfg.outputtype='wl';    % replay and get wl
+newcfg.replayweight = mmcdetweight(detp, newcfg.prop);
+newcfg.replaytime = mmcdettime(detp, newcfg.prop);
+newcfg.isnormalized = 0;
+newcfg.outputtype = 'wl';    % replay and get wl
 
 % now replay the detected photons
 
-[cube2,detp2]=mmclab(newcfg);
+[cube2, detp2] = mmclab(newcfg);
 
 % the two detected photon arrays should be the same. however, because
 % the program uses multi-threading, the orders may be different
 
-if(all(ismember(round(detp.data'*1e10)*1e-10,round(detp2.data'*1e10)*1e-10,'rows')))
-   disp('replay is successful :-)');
+if (all(ismember(round(detp.data' * 1e10) * 1e-10, round(detp2.data' * 1e10) * 1e-10, 'rows')))
+    disp('replay is successful :-)');
 else
-   disp('replay failed :-(');
+    disp('replay failed :-(');
 end
 
 % plot the Jacobian 3D profiles
 figure;
-plotmesh([cfg.node,log10(cube2.data)],cfg.elem(:,1:4),'z=0.2','linestyle','none');
+plotmesh([cfg.node, log10(cube2.data)], cfg.elem(:, 1:4), 'z=0.2', 'linestyle', 'none');
 hold on;
-plotmesh([cfg.node,log10(cube2.data)],cfg.elem(:,1:4),'x=30','linestyle','none');
-view(3)
-set(gca,'xlim',[0 60])
-set(gca,'ylim',[0 60])
-set(gca,'zlim',[0 60])
-shading interp
+plotmesh([cfg.node, log10(cube2.data)], cfg.elem(:, 1:4), 'x=30', 'linestyle', 'none');
+view(3);
+set(gca, 'xlim', [0 60]);
+set(gca, 'ylim', [0 60]);
+set(gca, 'zlim', [0 60]);
+shading interp;
 
 % set up for wp replay
 
-newcfg.outputtype='wp';    % replay and get wp
-[cube3,detp3,~,~]=mmclab(newcfg);
+newcfg.outputtype = 'wp';    % replay and get wp
+[cube3, detp3, ~, ~] = mmclab(newcfg);
 
 % the two detected photon arrays should be the same. however, because
 % the program uses multi-threading, the orders may be different
 
-if(all(ismember(round(detp.data'*1e10)*1e-10,round(detp3.data'*1e10)*1e-10,'rows')))
-   disp('replay is successful :-)');
+if (all(ismember(round(detp.data' * 1e10) * 1e-10, round(detp3.data' * 1e10) * 1e-10, 'rows')))
+    disp('replay is successful :-)');
 else
-   disp('replay failed :-(');
+    disp('replay failed :-(');
 end
 
 % plot the Jacobian 3D profiles
 figure;
-plotmesh([cfg.node,log10(cube3.data)],cfg.elem(:,1:4),'z=0.2','linestyle','none');
+plotmesh([cfg.node, log10(cube3.data)], cfg.elem(:, 1:4), 'z=0.2', 'linestyle', 'none');
 hold on;
-plotmesh([cfg.node,log10(cube3.data)],cfg.elem(:,1:4),'x=30','linestyle','none');
-view(3)
-set(gca,'xlim',[0 60])
-set(gca,'ylim',[0 60])
-set(gca,'zlim',[0 60])
-shading interp
\ No newline at end of file
+plotmesh([cfg.node, log10(cube3.data)], cfg.elem(:, 1:4), 'x=30', 'linestyle', 'none');
+view(3);
+set(gca, 'xlim', [0 60]);
+set(gca, 'ylim', [0 60]);
+set(gca, 'zlim', [0 60]);
+shading interp;
diff --git a/mmclab/example/demo_example_validation.m b/mmclab/example/demo_example_validation.m
index bfaa3988..e785d774 100644
--- a/mmclab/example/demo_example_validation.m
+++ b/mmclab/example/demo_example_validation.m
@@ -1,7 +1,7 @@
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% validate MMC with a homogeneous cubic domain
 %  (see MMC paper Fig. 2)
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %
 % In this example, we validate the MMCM algorithm using a homogeneous
 % cubic domain. This simulation generates the results
@@ -13,85 +13,85 @@
 % tddiffusion (for time-domain solutions) functions in the
 % package of Monte Carlo eXtreme (MCX) under the mcx/utils directory.
 %
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-%addpath('/Please/add/path/to/mcx/utils/')
+% addpath('/Please/add/path/to/mcx/utils/')
 addpath('../../matlab/');
 
-cfg.nphoton=3e6;
-cfg.seed=1648335518;
-[cfg.node,cfg.elem]=genT5mesh(0:2:60,0:2:60,0:2:60);
-cfg.elemprop=ones(size(cfg.elem,1),1);
-cfg.srcpos=[30.1,30.2,0];
-cfg.srcdir=[0 0 1];
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=1e-10;
-cfg.prop=[0 0 1 1;0.005 1.0 0.01 1.0];
-cfg.debuglevel='TP';
-cfg.isreflect=0;
-cfg.method='elem';
-
-cube=mmclab(cfg);
-%cube=mmclab(cfg,'sse'); % this is faster
-cube=cube.data;
-
-%%-----------------------------------------------------------------
+cfg.nphoton = 3e6;
+cfg.seed = 1648335518;
+[cfg.node, cfg.elem] = genT5mesh(0:2:60, 0:2:60, 0:2:60);
+cfg.elemprop = ones(size(cfg.elem, 1), 1);
+cfg.srcpos = [30.1, 30.2, 0];
+cfg.srcdir = [0 0 1];
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 1e-10;
+cfg.prop = [0 0 1 1; 0.005 1.0 0.01 1.0];
+cfg.debuglevel = 'TP';
+cfg.isreflect = 0;
+cfg.method = 'elem';
+
+cube = mmclab(cfg);
+% cube=mmclab(cfg,'sse'); % this is faster
+cube = cube.data;
+
+%% -----------------------------------------------------------------
 %% add paths to the necessary toolboxes
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-c0=299792458000;
+c0 = 299792458000;
 
-twin=[cfg.tstart+cfg.tstep/2:cfg.tstep:cfg.tend];
-gates=length(twin);
+twin = [cfg.tstart + cfg.tstep / 2:cfg.tstep:cfg.tend];
+gates = length(twin);
 
-cwcb=sum(cube,2);
-[cutpos,cutvalue,facedata]=qmeshcut(cfg.elem(:,1:4),cfg.node,cwcb,[0 30.2 0; 0 30.2 1; 1 30.2 0]);
+cwcb = sum(cube, 2);
+[cutpos, cutvalue, facedata] = qmeshcut(cfg.elem(:, 1:4), cfg.node, cwcb, [0 30.2 0; 0 30.2 1; 1 30.2 0]);
 
-[xi,yi]=meshgrid(0:2:60,0:2:60);
-vi=griddata(cutpos(:,1),cutpos(:,3),cutvalue,xi,yi);
+[xi, yi] = meshgrid(0:2:60, 0:2:60);
+vi = griddata(cutpos(:, 1), cutpos(:, 3), cutvalue, xi, yi);
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% plot the time-domain TPSF at [30 14 10]
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-figure
+figure;
 
-srcpos=[30.1,30.2,0];
-detpos=[30 14 10];
+srcpos = [30.1, 30.2, 0];
+detpos = [30 14 10];
 
-hold on
-semilogy((1:gates)/10,tddiffusion(0.005, 1, c0, 0, srcpos, detpos,twin),'r');
-idx=find(ismember(cfg.node,detpos,'rows'));
-semilogy((1:gates)/10,cube(idx,:),'+');
+hold on;
+semilogy((1:gates) / 10, tddiffusion(0.005, 1, c0, 0, srcpos, detpos, twin), 'r');
+idx = find(ismember(cfg.node, detpos, 'rows'));
+semilogy((1:gates) / 10, cube(idx, :), '+');
 
-set(gca,'fontsize',20)
-xlabel('t (ns)')
-ylabel('Fluence TPSF (1/mm^2)')
-set(gca,'yscale','log')
-legend('Diffusion','MMCM')
+set(gca, 'fontsize', 20);
+xlabel('t (ns)');
+ylabel('Fluence TPSF (1/mm^2)');
+set(gca, 'yscale', 'log');
+legend('Diffusion', 'MMCM');
 legend boxoff;
 box on;
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% generate a contour plot along y=30.2
-%%-----------------------------------------------------------------
-figure
+%% -----------------------------------------------------------------
+figure;
 clines = -1.5:-0.5:-8;
-[xi,yi]=meshgrid(0:2:60,0:2:60);
-srcs=[30.1,30.2,0];
-dets=[xi(:) 30.2*ones(size(xi(:))) yi(:)];
-phicw=reshape(cwdiffusion(0.005, 1.0, 0, srcs, dets),size(xi));
-
-hold on
-[c h2]=contour(xi,yi, log10(max(squeeze(phicw),1e-8)), -1.5:-0.5:-4, 'k-' );
-contour(xi,yi,log10(abs(vi*cfg.tstep)),clines,'r:')
-
-axis equal  
-set(gca,'xlim',[1 60])
-set(gca,'fontsize',20)
-xlabel('x (mm)')
-ylabel('z (mm)')
-legend('Diffusion','MMC')
+[xi, yi] = meshgrid(0:2:60, 0:2:60);
+srcs = [30.1, 30.2, 0];
+dets = [xi(:) 30.2 * ones(size(xi(:))) yi(:)];
+phicw = reshape(cwdiffusion(0.005, 1.0, 0, srcs, dets), size(xi));
+
+hold on;
+[c h2] = contour(xi, yi, log10(max(squeeze(phicw), 1e-8)), -1.5:-0.5:-4, 'k-');
+contour(xi, yi, log10(abs(vi * cfg.tstep)), clines, 'r:');
+
+axis equal;
+set(gca, 'xlim', [1 60]);
+set(gca, 'fontsize', 20);
+xlabel('x (mm)');
+ylabel('z (mm)');
+legend('Diffusion', 'MMC');
 legend boxoff;
 box on;
diff --git a/mmclab/example/demo_head_atlas.m b/mmclab/example/demo_head_atlas.m
index 30ede983..482a7391 100644
--- a/mmclab/example/demo_head_atlas.m
+++ b/mmclab/example/demo_head_atlas.m
@@ -1,108 +1,111 @@
-%%-----------------------------------------------------------------
-% In this example, we demonstrate light transport simulation in a mesh-based 
-% head atlas generated from the USC 19.5-year group atlas template[Sanchez2012]). 
+%% -----------------------------------------------------------------
+% In this example, we demonstrate light transport simulation in a mesh-based
+% head atlas generated from the USC 19.5-year group atlas template[Sanchez2012]).
 %
-% This script is a lightweight version of the DMMC[Yan2019] simulation demo used 
-% for Fig.9(a) in TranYan2019(submitted). For simplicity, a coarse mesh (lower  
+% This script is a lightweight version of the DMMC[Yan2019] simulation demo used
+% for Fig.9(a) in TranYan2019(submitted). For simplicity, a coarse mesh (lower
 % sampling rate) that represents part of the head(z>155) is simulated.
-% 
+%
 % [Sanchez2012] C.E.Sanchez J.E.Richards and C.R.Almli, “Age-Specific MRI Templates
 % for Pediatric Neuroimaging,” Developmental Neuropsychology 37, 379–399 (2012).
 %
-% [Yan2019] S.Yan, A.P.Tran, and Q.Fang, “Dual-grid mesh-based monte carlo algorithm  
-% for efficient photon transport simulations in complex three-dimensional media,” 
+% [Yan2019] S.Yan, A.P.Tran, and Q.Fang, “Dual-grid mesh-based monte carlo algorithm
+% for efficient photon transport simulations in complex three-dimensional media,”
 % Journal of Biomedical Optics 24(2), 020503 (2019).
 %
-% [TranYan2019] A.P.Tran, S.Yan and Q.Fang, "Improving model-based fNIRS 
+% [TranYan2019] A.P.Tran, S.Yan and Q.Fang, "Improving model-based fNIRS
 % analysis using mesh-based anatomical and light-transport models".
 %
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-clc
-clear
+clc;
+clear;
 load('head_atlas.mat');
 %% prepare cfg for MMCLAB simulation
-clear cfg
-cfg.nphoton=1e7; %takes ~240s on Intel i7-8700K(12 threads)
+clear cfg;
+cfg.nphoton = 1e7; % takes ~240s on Intel i7-8700K(12 threads)
 
-% medium labels:0-ambient air,1-air cavities,2-scalp,3-skull,4-csf,5-gray matter,6-white matter 
-cfg.node=double(node);
-cfg.elem=double(elem);
-cfg.elemprop=double(prop);
-cfg.prop=[0,0,1,1;0,0,1,1;0.019 7.8 0.89 1.37;0.019 7.8 0.89 1.37;0.004 0.009 0.89 1.37;0.02 9.0 0.89 1.37;0.08 40.9 0.84 1.37];
+% medium labels:0-ambient air,1-air cavities,2-scalp,3-skull,4-csf,5-gray matter,6-white matter
+cfg.node = double(node);
+cfg.elem = double(elem);
+cfg.elemprop = double(prop);
+cfg.prop = [0, 0, 1, 1; 0, 0, 1, 1; 0.019 7.8 0.89 1.37; 0.019 7.8 0.89 1.37; 0.004 0.009 0.89 1.37; 0.02 9.0 0.89 1.37; 0.08 40.9 0.84 1.37];
 
 % light source
-cfg.srctype='pencil';
-cfg.srcdir=[-0.5086,-0.1822,-0.8415]; %inward-pointing source
-cfg.srcpos=[133.5370,90.1988,200.0700]; %pencil beam source placed at EEG 10-5 landmark:"C4h"
-    cfg.srcpos=cfg.srcpos+0.001*cfg.srcdir; %ensure source is inside the mesh
+cfg.srctype = 'pencil';
+cfg.srcdir = [-0.5086, -0.1822, -0.8415]; % inward-pointing source
+cfg.srcpos = [133.5370, 90.1988, 200.0700]; % pencil beam source placed at EEG 10-5 landmark:"C4h"
+cfg.srcpos = cfg.srcpos + 0.001 * cfg.srcdir; % ensure source is inside the mesh
 
 % time windows
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=5e-10;
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 5e-10;
 
 % other simulation parameters
-cfg.isreflect=1;
-cfg.debuglevel='TP';
-cfg.method='grid'; %DMMC mode
+cfg.isreflect = 1;
+cfg.debuglevel = 'TP';
+cfg.method = 'grid'; % DMMC mode
 
 %% run mmc simulation
-[flux]=mmclab(cfg);
+[flux] = mmclab(cfg);
 
 %% post-simulation data processing and visualization
 % convert time-resolved fluence to CW fluence
-CWfluence=sum(flux.data*cfg.tstep,4); 
+CWfluence = sum(flux.data * cfg.tstep, 4);
 
 % coronal plane selected for fluence plot
-y_plane=90.5;   
+y_plane = 90.5;
 
 % fix spatial offset between the coordinate origins of DMMC AABB and the mesh
-DMMC_AABB_origin=min(cfg.node); %spatial offset of the DMMC AABB
-DMMC_voxel_origin=DMMC_AABB_origin+0.5; %centroid of the 1st voxel for DMMC AABB
-DMMC_AABB_dimension=size(CWfluence);
-CWfluence_DMMC=squeeze(CWfluence(:,ceil(y_plane-DMMC_AABB_origin(1,2)),:)); %along y-axis, DMMC AABB happens to have an offset very close to 3(2.9955)
-[xx,zz]=meshgrid(DMMC_voxel_origin(1,1):(DMMC_voxel_origin(1,1)+DMMC_AABB_dimension(1,1)-1),DMMC_voxel_origin(1,3):(DMMC_voxel_origin(1,3)+DMMC_AABB_dimension(1,3)-1));
+DMMC_AABB_origin = min(cfg.node); % spatial offset of the DMMC AABB
+DMMC_voxel_origin = DMMC_AABB_origin + 0.5; % centroid of the 1st voxel for DMMC AABB
+DMMC_AABB_dimension = size(CWfluence);
+CWfluence_DMMC = squeeze(CWfluence(:, ceil(y_plane - DMMC_AABB_origin(1, 2)), :)); % along y-axis, DMMC AABB happens to have an offset very close to 3(2.9955)
+[xx, zz] = meshgrid(DMMC_voxel_origin(1, 1):(DMMC_voxel_origin(1, 1) + DMMC_AABB_dimension(1, 1) - 1), DMMC_voxel_origin(1, 3):(DMMC_voxel_origin(1, 3) + DMMC_AABB_dimension(1, 3) - 1));
 
 figure;
-clines=-20:0.5:0;
-contourf(xx,zz,log10(abs(CWfluence_DMMC')),clines,'linestyle','--','color','w','linewidth',1.5,'DisplayName','DMMC');
-hold on;axis equal;
+clines = -20:0.5:0;
+contourf(xx, zz, log10(abs(CWfluence_DMMC')), clines, 'linestyle', '--', 'color', 'w', 'linewidth', 1.5, 'DisplayName', 'DMMC');
+hold on;
+axis equal;
 colorbar('EastOutside');
 
 % plot tissue boundaries, auxiliary functions are part of iso2mesh(http://iso2mesh.sf.net)
-plane=[0 y_plane 0; 0 y_plane 1; 1 y_plane 0];
-label=unique(prop);
-face=[];
-for i=1:2:size(label,1)
-    newface=volface(cfg.elem(prop==label(i),:));
-    face=[face;newface];
+plane = [0 y_plane 0; 0 y_plane 1; 1 y_plane 0];
+label = unique(prop);
+face = [];
+for i = 1:2:size(label, 1)
+    newface = volface(cfg.elem(prop == label(i), :));
+    face = [face; newface];
 end
-[cutpos,cutvalue,cutedges]=qmeshcut(face(:,1:3),node,node(:,1),plane);
-[cutpos,cutedges]=removedupnodes(cutpos,cutedges);
-cutloop=extractloops(cutedges);
-[nanidx]=find(isnan(cutloop));
+[cutpos, cutvalue, cutedges] = qmeshcut(face(:, 1:3), node, node(:, 1), plane);
+[cutpos, cutedges] = removedupnodes(cutpos, cutedges);
+cutloop = extractloops(cutedges);
+[nanidx] = find(isnan(cutloop));
 
-for i=1:size(nanidx,2)
-    if(i==9) 
-        continue;
+for i = 1:size(nanidx, 2)
+    if (i == 9)
+        continue
     end
-    if(i==1)
-        plot(cutpos(cutloop(1:(nanidx(i)-1)),1),cutpos(cutloop(1:(nanidx(i)-1)),3),'linestyle','--','color','k','LineWidth',1.25,'HandleVisibility','off');
-    elseif(i==2)
-        plot(cutpos(cutloop((nanidx(i-1)+1):(nanidx(i)-1)),1),cutpos(cutloop((nanidx(i-1)+1):(nanidx(i)-1)),3),'linestyle','--','color','k','LineWidth',1.25,'HandleVisibility','off');
+    if (i == 1)
+        plot(cutpos(cutloop(1:(nanidx(i) - 1)), 1), cutpos(cutloop(1:(nanidx(i) - 1)), 3), 'linestyle', '--', 'color', 'k', 'LineWidth', 1.25, 'HandleVisibility', 'off');
+    elseif (i == 2)
+        plot(cutpos(cutloop((nanidx(i - 1) + 1):(nanidx(i) - 1)), 1), cutpos(cutloop((nanidx(i - 1) + 1):(nanidx(i) - 1)), 3), 'linestyle', '--', 'color', 'k', 'LineWidth', 1.25, 'HandleVisibility', 'off');
     else
-        plot(cutpos(cutloop((nanidx(i-1)+1):(nanidx(i)-1)),1),cutpos(cutloop((nanidx(i-1)+1):(nanidx(i)-1)),3),'linestyle','--','color','k','LineWidth',1.25,'HandleVisibility','off');
+        plot(cutpos(cutloop((nanidx(i - 1) + 1):(nanidx(i) - 1)), 1), cutpos(cutloop((nanidx(i - 1) + 1):(nanidx(i) - 1)), 3), 'linestyle', '--', 'color', 'k', 'LineWidth', 1.25, 'HandleVisibility', 'off');
     end
 end
 
 % plot source, legend, etc.
-plot(cfg.srcpos(1,1),cfg.srcpos(1,3),'o','MarkerEdgeColor','r','MarkerFaceColor','r','MarkerSize',10,'DisplayName','source');
-lg=legend('Location','northeast');
-set(lg,'color','[0.85 0.85 0.85]');
-set(lg,'box','on');
-set(gca,'ylim', [160 225]);ylabel('z [mm]');
-set(gca,'xlim', [10 165]);xlabel('x [mm]');
-set(gca,'clim',[-12 0]);
-set(gca,'fontsize',18);
-set(gca, 'FontName', 'Times New Roman');
\ No newline at end of file
+plot(cfg.srcpos(1, 1), cfg.srcpos(1, 3), 'o', 'MarkerEdgeColor', 'r', 'MarkerFaceColor', 'r', 'MarkerSize', 10, 'DisplayName', 'source');
+lg = legend('Location', 'northeast');
+set(lg, 'color', '[0.85 0.85 0.85]');
+set(lg, 'box', 'on');
+set(gca, 'ylim', [160 225]);
+ylabel('z [mm]');
+set(gca, 'xlim', [10 165]);
+xlabel('x [mm]');
+set(gca, 'clim', [-12 0]);
+set(gca, 'fontsize', 18);
+set(gca, 'FontName', 'Times New Roman');
diff --git a/mmclab/example/demo_immc_basic.m b/mmclab/example/demo_immc_basic.m
index a6539d57..5fa8b87b 100644
--- a/mmclab/example/demo_immc_basic.m
+++ b/mmclab/example/demo_immc_basic.m
@@ -2,7 +2,7 @@
 % same as three benchmarks in the paper: https://doi.org/10.1364/BOE.411898
 %
 % For iMMC, you need to edit cfg.elem and cfg.node. Extra data is needed to
-% run iMMC. The data formats of cfg.elem and cfg.node for iMMC are shown 
+% run iMMC. The data formats of cfg.elem and cfg.node for iMMC are shown
 % below:
 %% edge-based iMMC (e-iMMC)
 %
@@ -22,110 +22,110 @@
 
 %% add path
 % 1. you need to add the path to iso2mesh toolbox if not already
-%addpath('/path/to/iso2mesh/toolbox/');
+% addpath('/path/to/iso2mesh/toolbox/');
 
 % 2. you need to add the path to MMC matlab folder
-addpath('../../matlab')
+addpath('../../matlab');
 
 %% edge-based iMMC, benchmark B1
 
 % (a) generate bounding box and insert edge
-[nbox,ebox]=meshgrid6(0:1,0:1,0:1);
-fbox=volface(ebox);
-EPS=0.001;
-nbox=[nbox; [1-EPS 0.5 0.5]; [EPS 0.5 0.5]];  % insert new nodes (node 9 and 10)
-fbox=[fbox; [9 9 10]];  % insert new edge coneected by node 9 and 10
+[nbox, ebox] = meshgrid6(0:1, 0:1, 0:1);
+fbox = volface(ebox);
+EPS = 0.001;
+nbox = [nbox; [1 - EPS 0.5 0.5]; [EPS 0.5 0.5]];  % insert new nodes (node 9 and 10)
+fbox = [fbox; [9 9 10]];  % insert new edge coneected by node 9 and 10
 
 clear cfg0 cfg;
 
-cfg0.nphoton=1e6;
-cfg0.srcpos=[0.5 0.5 1];
-cfg0.srcdir=[0 0 -1];
-cfg0.prop=[0 0 1 1;0.0458 35.6541 0.9000 1.3700; 23.0543 9.3985 0.9000 1.3700];
-cfg0.tstart=0;
-cfg0.tend=5e-9;
-cfg0.tstep=5e-9;
-cfg0.debuglevel='TP';
-cfg0.method='grid';
-cfg0.steps=[0.01 0.01 0.01];
-cfg0.isreflect=1;
-cfg0.gpuid=-1;
-
-
-cfg=cfg0;
+cfg0.nphoton = 1e6;
+cfg0.srcpos = [0.5 0.5 1];
+cfg0.srcdir = [0 0 -1];
+cfg0.prop = [0 0 1 1; 0.0458 35.6541 0.9000 1.3700; 23.0543 9.3985 0.9000 1.3700];
+cfg0.tstart = 0;
+cfg0.tend = 5e-9;
+cfg0.tstep = 5e-9;
+cfg0.debuglevel = 'TP';
+cfg0.method = 'grid';
+cfg0.steps = [0.01 0.01 0.01];
+cfg0.isreflect = 1;
+cfg0.gpuid = -1;
+
+cfg = cfg0;
 
 % (b) generate mesh
-[cfg.node,cfg.elem]=s2m(nbox,num2cell(fbox,2),1,100,'tetgen1.5',[],[],'-YY');
-cfg.elemprop=ones(size(cfg.elem,1),1);
+[cfg.node, cfg.elem] = s2m(nbox, num2cell(fbox, 2), 1, 100, 'tetgen1.5', [], [], '-YY');
+cfg.elemprop = ones(size(cfg.elem, 1), 1);
 
 % (c) label the edge that has node 9 and 10 and add radii
 
 % find all elements that contains special edge between nodes 9-10
-edgeid=reshape(ismember(sort(meshedge(cfg.elem),2),[9 10],'rows'),[size(cfg.elem,1),6]);
+edgeid = reshape(ismember(sort(meshedge(cfg.elem), 2), [9 10], 'rows'), [size(cfg.elem, 1), 6]);
 
 % create the edgeroi input - every appearance of that edge, we define its radius
-cfg.edgeroi=zeros(size(cfg.elem,1),6);
-cfg.edgeroi(edgeid)=0.1;
-
-cfg.noderoi=zeros(size(cfg.node,1),1);
-cfg.noderoi(9)=0.1;
+cfg.edgeroi = zeros(size(cfg.elem, 1), 6);
+cfg.edgeroi(edgeid) = 0.1;
 
+cfg.noderoi = zeros(size(cfg.node, 1), 1);
+cfg.noderoi(9) = 0.1;
 
 % run edge-based iMMC
-flux_eimmc=mmclab(cfg);
+flux_eimmc = mmclab(cfg);
 
 %% node-based iMMC, benchmark B2
 
 % (a) generate bounding box and insert edge
-[nbox,ebox]=meshgrid6(0:1,0:1,0:1);
-fbox=volface(ebox);
-nbox=[nbox; [0.5 0.5 0.5]];  % insert new nodes (node 9)
+[nbox, ebox] = meshgrid6(0:1, 0:1, 0:1);
+fbox = volface(ebox);
+nbox = [nbox; [0.5 0.5 0.5]];  % insert new nodes (node 9)
 
-cfg=cfg0;
+cfg = cfg0;
 
 % (b) generate mesh
-[cfg.node,cfg.elem]=s2m(nbox,num2cell(fbox,2),1,100,'tetgen1.5',[],[],'-YY');
-cfg.elemprop=ones(size(cfg.elem,1),1);
+[cfg.node, cfg.elem] = s2m(nbox, num2cell(fbox, 2), 1, 100, 'tetgen1.5', [], [], '-YY');
+cfg.elemprop = ones(size(cfg.elem, 1), 1);
 
 % (c) label the edge that has node 9 and 10 and add radii
-cfg.noderoi=zeros(size(cfg.node,1),1);
-cfg.noderoi(9)=0.1;
+cfg.noderoi = zeros(size(cfg.node, 1), 1);
+cfg.noderoi(9) = 0.1;
 
 % run node-based iMMC
-flux_nimmc=mmclab(cfg);
-
+flux_nimmc = mmclab(cfg);
 
 %% face-based iMMC, benchmark B3
 
-cfg=cfg0;
+cfg = cfg0;
 
 % (a) generate bounding box and insert edge
-[cfg.node,cfg.elem]=meshgrid6(0:1,0:1,0:1);
-cfg.elemprop=ones(size(cfg.elem,1),1);
+[cfg.node, cfg.elem] = meshgrid6(0:1, 0:1, 0:1);
+cfg.elemprop = ones(size(cfg.elem, 1), 1);
 
 % generate all triangular faces, label the top two triangles at z=1 as
 % faceroi and define a h=0.1mm thin-membrane
-facelist=nchoosek(1:4,3);
-allfaces=[];
-for i=1:length(facelist)
-   allfaces=[allfaces;cfg.elem(:,facelist(i,:))];
+facelist = nchoosek(1:4, 3);
+allfaces = [];
+for i = 1:length(facelist)
+    allfaces = [allfaces; cfg.elem(:, facelist(i, :))];
 end
 
 % sum(allfaces>4,2)==3 gives the triangles that are made of nodes 5/6/7/8
-cfg.faceroi=reshape(double(sum(allfaces>4,2)==3), size(cfg.elem,1),size(facelist,1));
-cfg.faceroi(cfg.faceroi>0)=0.1;
+cfg.faceroi = reshape(double(sum(allfaces > 4, 2) == 3), size(cfg.elem, 1), size(facelist, 1));
+cfg.faceroi(cfg.faceroi > 0) = 0.1;
 
 % run node-based iMMC
-flux_fimmc=mmclab(cfg);
+flux_fimmc = mmclab(cfg);
 
 %% plot the results
-figure,
-subplot(131)
-imagesc(log10(rot90(squeeze(flux_eimmc.data(50,1:100,1:100)))))
-title('edge-iMMC');axis equal
-subplot(132)
-imagesc(log10(rot90(squeeze(flux_nimmc.data(50,1:100,1:100)))))
-title('node-iMMC');axis equal
-subplot(133)
-imagesc(log10(rot90(squeeze(abs(flux_fimmc.data(50,1:100,1:100))))))
-title('face-iMMC');axis equal
+figure;
+subplot(131);
+imagesc(log10(rot90(squeeze(flux_eimmc.data(50, 1:100, 1:100)))));
+title('edge-iMMC');
+axis equal;
+subplot(132);
+imagesc(log10(rot90(squeeze(flux_nimmc.data(50, 1:100, 1:100)))));
+title('node-iMMC');
+axis equal;
+subplot(133);
+imagesc(log10(rot90(squeeze(abs(flux_fimmc.data(50, 1:100, 1:100))))));
+title('face-iMMC');
+axis equal;
diff --git a/mmclab/example/demo_immc_vessel.m b/mmclab/example/demo_immc_vessel.m
index 7d71f907..baf7ba80 100644
--- a/mmclab/example/demo_immc_vessel.m
+++ b/mmclab/example/demo_immc_vessel.m
@@ -1,4 +1,4 @@
-function [cfg, flux]=demo_immc_vessel(cfg)
+function [cfg, flux] = demo_immc_vessel(cfg)
 % This example shows how to run e-iMMC on a vessel network
 
 %% load vessel data
@@ -8,105 +8,105 @@
 % nbox:   nodes of bounding box
 % fbox:   faces of bounding box
 
-%addpath('/path/to/iso2mesh/toolbox/');
+% addpath('/path/to/iso2mesh/toolbox/');
 
-if(nargin==0)
+if (nargin == 0)
 
-    vs=load('vessel.mat');
+    vs = load('vessel.mat');
 
-    edge=vs.edge;   % vessel edges
-    fbox=vs.fbox;   % bounding box faces
-    nbox=vs.nbox;   % bounding box nodes
-    node=vs.node;   % nodes on the vessel network
-    noder=vs.noder; % nodal radius of each node
+    edge = vs.edge;   % vessel edges
+    fbox = vs.fbox;   % bounding box faces
+    nbox = vs.nbox;   % bounding box nodes
+    node = vs.node;   % nodes on the vessel network
+    noder = vs.noder; % nodal radius of each node
 
     clear vs;
 
     %% 1. Mesh generation
 
     % (a) add the bounding box (nbox and fbox) into node and face
-    offset=size(nbox,1);
-    edge=edge+offset;  % change the node index after inserting bounding box
-    noder=[zeros(offset,1); noder];  % add offset into noder
-    node=[nbox; node];  % add nodes of bounding box into node
-    fedge=[edge(:,1) edge];  %  convert edge to face for mesh generation
-    face=[fbox; fedge];  %  add faces of bounding box into face
+    offset = size(nbox, 1);
+    edge = edge + offset;  % change the node index after inserting bounding box
+    noder = [zeros(offset, 1); noder];  % add offset into noder
+    node = [nbox; node];  % add nodes of bounding box into node
+    fedge = [edge(:, 1) edge];  %  convert edge to face for mesh generation
+    face = [fbox; fedge];  %  add faces of bounding box into face
 
     % (b) generate .poly file
     % vnode, velem: nodes and elements for generated mesh
-    [vnode, velem]=s2m(node,num2cell(face,2),1,100,'tetgen1.5',[],[],'-YY');
+    [vnode, velem] = s2m(node, num2cell(face, 2), 1, 100, 'tetgen1.5', [], [], '-YY');
 
     %% 2. Create edgeroi
     % (a) get mapping from edge to radius (you can build your own e2r)
-    e2r=edge2radius(edge,noder);
+    e2r = edge2radius(edge, noder);
     % (b) get edgeroi
-    [vnode,velem,eroi]=edgeroi(vnode,velem,e2r);
+    [vnode, velem, eroi] = edgeroi(vnode, velem, e2r);
 
     %% 3. Run mmc
 
-    res=0.001;  % resolution: 0.001mm
-    cfg.nphoton=1e6;
-    cfg.srctype='pencil';
-    cfg.srcpos=[150.5 150.5 605]*res;
-    cfg.srcdir=[0 0 -1];
-    cfg.elemprop=ones(size(velem,1),1);
-    cfg.prop=[0 0 1 1;
-        0.0458   35.6541    0.9000    1.3700;   % dermis
-        23.0543    9.3985    0.9000    1.3700]; % blood
-    cfg.tstart=0;
-    cfg.tend=5e-9;
-    cfg.tstep=5e-9;
-    cfg.debuglevel='TP';
-    cfg.method='grid';
-    cfg.steps=[0.001 0.001 0.001];
-    cfg.gpuid=-1;
-    cfg.isreflect=1;
-    cfg.outputtype='energy';
-    
-    cfg.elem=velem;
-    cfg.node=vnode*res;
-    cfg.edgeroi=eroi*res;
-    cfg.noderoi=zeros(size(vnode,1),1);
-    cfg.noderoi(1:size(noder,1))=noder*res;
+    res = 0.001;  % resolution: 0.001mm
+    cfg.nphoton = 1e6;
+    cfg.srctype = 'pencil';
+    cfg.srcpos = [150.5 150.5 605] * res;
+    cfg.srcdir = [0 0 -1];
+    cfg.elemprop = ones(size(velem, 1), 1);
+    cfg.prop = [0 0 1 1
+                0.0458   35.6541    0.9000    1.3700    % dermis
+                23.0543    9.3985    0.9000    1.3700]; % blood
+    cfg.tstart = 0;
+    cfg.tend = 5e-9;
+    cfg.tstep = 5e-9;
+    cfg.debuglevel = 'TP';
+    cfg.method = 'grid';
+    cfg.steps = [0.001 0.001 0.001];
+    cfg.gpuid = -1;
+    cfg.isreflect = 1;
+    cfg.outputtype = 'energy';
+
+    cfg.elem = velem;
+    cfg.node = vnode * res;
+    cfg.edgeroi = eroi * res;
+    cfg.noderoi = zeros(size(vnode, 1), 1);
+    cfg.noderoi(1:size(noder, 1)) = noder * res;
 end
 
-tic
-flux=mmclab(cfg);
-toc
+tic;
+flux = mmclab(cfg);
+toc;
 
 %% plotting
-figure,imagesc(log10(rot90(squeeze(flux.data(:,150,:)))))
+figure;
+imagesc(log10(rot90(squeeze(flux.data(:, 150, :)))));
 axis equal;
 title('energy deposition map');
 
-
 %% function: get vessel radii
-function e2r = edge2radius(edge,noder)
+function e2r = edge2radius(edge, noder)
 
 % vr = vesselradii(edge,noder)
-% 
+%
 % get the radii for the input edges (vessels)
-% 
+%
 % input:
 %     edge: ne x 2 array. ne is the total number of edges. 2 columns represent
 %     the indices of nodes connecting the edges
-%     noder: nr x 1 array storing the radius of each node. nr is the total 
+%     noder: nr x 1 array storing the radius of each node. nr is the total
 %     number of nodes
 % output:
 %     vr: ne x 1 array storing the radius of each edge
 
-e2r=java.util.HashMap;  % set storing all vessel edges
-edge=sort(edge,2);
-for i=1:size(edge,1)
-    vr=max([noder(edge(i,1)),noder(edge(i,2))]);
-    e2r.put(num2str(edge(i,:)),vr);
+e2r = java.util.HashMap;  % set storing all vessel edges
+edge = sort(edge, 2);
+for i = 1:size(edge, 1)
+    vr = max([noder(edge(i, 1)), noder(edge(i, 2))]);
+    e2r.put(num2str(edge(i, :)), vr);
 end
 
 %% function: get edgeroi
-function [node,elem,eroi]=edgeroi(node,elem,e2r)
-% 
+function [node, elem, eroi] = edgeroi(node, elem, e2r)
+%
 % build the edgeroi for iMMC
-% 
+%
 % input:
 %     node: node coordinates for elem
 %     elem: input mesh containing the edges
@@ -117,75 +117,75 @@
 %          To build the mapping, you should do
 %          e2r.put(num2str(edge),radius)
 % output:
-%     eroi: ne x 6 array, storing the cylindrial edge-roi radii in the 
-%           nchoosek order [(1,2),(1,3),(1,4),(2,3),(2,4),(3,4)]. 
+%     eroi: ne x 6 array, storing the cylindrial edge-roi radii in the
+%           nchoosek order [(1,2),(1,3),(1,4),(2,3),(2,4),(3,4)].
 %           A 0 indicates no ROI. Up to 2 edges are supported
 
-eo=[1 2; 1 3; 1 4; 2 3; 2 4; 3 4]; % edge order in an element
-eroi = zeros(size(elem,1),6);
+eo = [1 2; 1 3; 1 4; 2 3; 2 4; 3 4]; % edge order in an element
+eroi = zeros(size(elem, 1), 6);
 
-i=1;
-while i<=size(elem,1)
+i = 1;
+while i <= size(elem, 1)
     enum = 0; % number of edges being labeled
-    for j=1:6
-        edge=sort([elem(i,eo(j,1)) elem(i,eo(j,2))]);
+    for j = 1:6
+        edge = sort([elem(i, eo(j, 1)) elem(i, eo(j, 2))]);
         if e2r.containsKey(num2str(edge))
-            eroi(i,j)=e2r.get(num2str(edge));
-            enum=enum+1;
+            eroi(i, j) = e2r.get(num2str(edge));
+            enum = enum + 1;
         end
     end
-    
-    if enum>2
-        % if there are more than 2 labeled edges,split and relabel the 
+
+    if enum > 2
+        % if there are more than 2 labeled edges,split and relabel the
         % current element
-        [node,elem,eroi]=splitelem(node,elem,eroi,e2r,i);
-        i=i+3; % replace the old element with four new elements
+        [node, elem, eroi] = splitelem(node, elem, eroi, e2r, i);
+        i = i + 3; % replace the old element with four new elements
     end
-    
-    i=i+1;
+
+    i = i + 1;
 end
 
 %% function
-function [node,elem,eroi]=splitelem(node,elem,eroi,e2r,index)
-% 
+function [node, elem, eroi] = splitelem(node, elem, eroi, e2r, index)
+%
 % split the element that has over 2 labeled edges
-% 
+%
 % input:
 %     node:  node coordinates for elem
 %     elem:  input mesh containing the edges
 %     eroi:  input data for cfg.edgeroi
 %     e2r:   java.util.HashMap mapping edge to its radius
 %     index: index of element that needs to be split
-% 
+%
 % output:
 %     elem:  mesh after spliting
 
-eo=[1 2; 1 3; 1 4; 2 3; 2 4; 3 4]; % edge order in an element
-fo=[1 2 3; 1 2 4; 1 3 4; 2 3 4]; % face order in an element
-
-selem=elem(index,:); % element to be split
-c=meshcentroid(node,selem); % centroid of the element to be split
-cindex=size(node,1)+1;
-node=[node; c]; % put the centroid in the end
-
-newelem=[]; % 4 elements that have been split using centroid
-newroi=[];  % new edge roi
-for i=1:size(fo,1)
-    e=[selem(fo(i,1)) selem(fo(i,2)) selem(fo(i,3)) cindex];
-    newelem=[newelem; e];
-    
-    r=zeros(1,size(eo,1));
+eo = [1 2; 1 3; 1 4; 2 3; 2 4; 3 4]; % edge order in an element
+fo = [1 2 3; 1 2 4; 1 3 4; 2 3 4]; % face order in an element
+
+selem = elem(index, :); % element to be split
+c = meshcentroid(node, selem); % centroid of the element to be split
+cindex = size(node, 1) + 1;
+node = [node; c]; % put the centroid in the end
+
+newelem = []; % 4 elements that have been split using centroid
+newroi = [];  % new edge roi
+for i = 1:size(fo, 1)
+    e = [selem(fo(i, 1)) selem(fo(i, 2)) selem(fo(i, 3)) cindex];
+    newelem = [newelem; e];
+
+    r = zeros(1, size(eo, 1));
     % check the edge that has radius and fill it in edgeroi
-    for j=1:size(eo,1)
-        edge=sort([e(eo(j,1)),e(eo(j,2))]);
+    for j = 1:size(eo, 1)
+        edge = sort([e(eo(j, 1)), e(eo(j, 2))]);
         if e2r.containsKey(num2str(edge))
-            r(j)=e2r.get(num2str(edge));
+            r(j) = e2r.get(num2str(edge));
         end
     end
-    newroi=[newroi; r];
+    newroi = [newroi; r];
 end
 
 % remove the old element and insert the new elements
-elem=[elem(1:index-1,:); newelem; elem(index+1:end,:)];
+elem = [elem(1:index - 1, :); newelem; elem(index + 1:end, :)];
 % remove the old roi and insert the new rois
-eroi=[eroi(1:index-1,:); newroi; eroi(index+1:end,:)];
\ No newline at end of file
+eroi = [eroi(1:index - 1, :); newroi; eroi(index + 1:end, :)];
diff --git a/mmclab/example/demo_mcxyz_skinvessel.m b/mmclab/example/demo_mcxyz_skinvessel.m
index 66f2291b..2ff18e77 100644
--- a/mmclab/example/demo_mcxyz_skinvessel.m
+++ b/mmclab/example/demo_mcxyz_skinvessel.m
@@ -6,90 +6,89 @@
 %  higher absorption (~42%) with boundaryflag=2
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-clear cfg flux
+clear cfg flux;
 
 %% create the skin-vessel benchmark mesh
-[no,fc]=latticegrid([0 200],[0 200],[20 32 200]); % create a 3-layer tissue
-no(end,:)=no(end,:)+1e-5;
+[no, fc] = latticegrid([0 200], [0 200], [20 32 200]); % create a 3-layer tissue
+no(end, :) = no(end, :) + 1e-5;
 
-fc2=cell2mat(fc);
-fc=[fc2(:,[1 2 3]); fc2(:,[1 3 4])];
+fc2 = cell2mat(fc);
+fc = [fc2(:, [1 2 3]); fc2(:, [1 3 4])];
 
-[ncy,fcy]=meshacylinder([-1,99.5,99.5],[201,99.5,99.5],20,5); % add the vessel
-[newnode,newelem]=surfboolean(no,fc,'first',ncy,fcy);  % merge the two domains
+[ncy, fcy] = meshacylinder([-1, 99.5, 99.5], [201, 99.5, 99.5], 20, 5); % add the vessel
+[newnode, newelem] = surfboolean(no, fc, 'first', ncy, fcy);  % merge the two domains
 
-c0=[10,100,150,26]';
-seeds=[ones(4,2)*100, c0];  % define the regions by index
+c0 = [10, 100, 150, 26]';
+seeds = [ones(4, 2) * 100, c0];  % define the regions by index
 
-%ISO2MESH_TETGENOPT='-Y -A'
-[cfg.node,cfg.elem]=s2m(newnode,newelem(:,1:3),1,30,'tetgen',seeds,[]); % creating the merged mesh domain
+% ISO2MESH_TETGENOPT='-Y -A'
+[cfg.node, cfg.elem] = s2m(newnode, newelem(:, 1:3), 1, 30, 'tetgen', seeds, []); % creating the merged mesh domain
 
-cfg.unitinmm=0.005;
-cfg.method='elem';
+cfg.unitinmm = 0.005;
+cfg.method = 'elem';
 
 figure;
 subplot(121);
-plotmesh(cfg.node,cfg.elem);
+plotmesh(cfg.node, cfg.elem);
 
-cfg.elemprop=cfg.elem(:,5);
-cfg.elem=cfg.elem(:,1:4);
+cfg.elemprop = cfg.elem(:, 5);
+cfg.elem = cfg.elem(:, 1:4);
 
 %% define other properties
 
-cfg.prop=[0.0000         0.0    1.0000    1
-    3.5640e-05    1.0000    1.0000    1.3700
-   23.0543    9.3985    0.9000    1.3700
-    0.0458   35.6541    0.9000    1.3700
-    1.6572   37.5940    0.9000    1.3700];
+cfg.prop = [0.0000         0.0    1.0000    1
+            3.5640e-05    1.0000    1.0000    1.3700
+            23.0543    9.3985    0.9000    1.3700
+            0.0458   35.6541    0.9000    1.3700
+            1.6572   37.5940    0.9000    1.3700];
 
-cfg.srcpos=[100 100 -1];
-cfg.srcdir=[0 0 1];
+cfg.srcpos = [100 100 -1];
+cfg.srcdir = [0 0 1];
 
-cfg.tstart=0;
-cfg.tend=5e-8;
-cfg.tstep=5e-8;
+cfg.tstart = 0;
+cfg.tend = 5e-8;
+cfg.tstep = 5e-8;
 % cfg.outputtype='energy'; %energy deposition in mmc varys with elem volume
-cfg.outputtype='flux';
-cfg.minenergy=0.01;
+cfg.outputtype = 'flux';
+cfg.minenergy = 0.01;
 
-cfg.srctype='disk';
-cfg.srcparam1=[0.3 0 0 0]/cfg.unitinmm; % in grid unit
+cfg.srctype = 'disk';
+cfg.srcparam1 = [0.3 0 0 0] / cfg.unitinmm; % in grid unit
 
 %% define wide-field disk source by extending the mesh to the widefield src
-srcdef=struct('srctype',cfg.srctype,'srcpos',cfg.srcpos,'srcdir',cfg.srcdir,...
-    'srcparam1',cfg.srcparam1,'srcparam2',[]);
+srcdef = struct('srctype', cfg.srctype, 'srcpos', cfg.srcpos, 'srcdir', cfg.srcdir, ...
+                'srcparam1', cfg.srcparam1, 'srcparam2', []);
 
-[cfg.node,cfg.elem] = mmcaddsrc(cfg.node,[cfg.elem cfg.elemprop],...
-    mmcsrcdomain(srcdef,[min(cfg.node);max(cfg.node)]));
+[cfg.node, cfg.elem] = mmcaddsrc(cfg.node, [cfg.elem cfg.elemprop], ...
+                                 mmcsrcdomain(srcdef, [min(cfg.node); max(cfg.node)]));
 
-
-cfg.elemprop=cfg.elem(:,5);
-cfg.elem=cfg.elem(:,1:4);
+cfg.elemprop = cfg.elem(:, 5);
+cfg.elem = cfg.elem(:, 1:4);
 
 %% other simulation information
 
-cfg.nphoton=1e7;
-cfg.seed=1648335518;
+cfg.nphoton = 1e7;
+cfg.seed = 1648335518;
 
-cfg.debuglevel='TP';
-cfg.isreflect=0;
+cfg.debuglevel = 'TP';
+cfg.isreflect = 0;
 
 %% mmc simulation
 
-flux=mmclab(cfg);
-flux=flux.data;
-fluxcw=sum(flux,2)*cfg.tstep*100; % multiplying 100 converts 1/mm^2 to 1/cm^2 to match mcxyz output
+flux = mmclab(cfg);
+flux = flux.data;
+fluxcw = sum(flux, 2) * cfg.tstep * 100; % multiplying 100 converts 1/mm^2 to 1/cm^2 to match mcxyz output
 
 %% plot simulated photon profiles
 
 subplot(122);
 hold on;
-qmeshcut(cfg.elem(cfg.elemprop>0,1:4),cfg.node*cfg.unitinmm,log10(fluxcw),'x=0.5','linestyle','none');
+qmeshcut(cfg.elem(cfg.elemprop > 0, 1:4), cfg.node * cfg.unitinmm, log10(fluxcw), 'x=0.5', 'linestyle', 'none');
 view([1 0 0]);
-set(gca,'zlim',[0 1],'ylim',[0 1],'zdir','reverse')
+set(gca, 'zlim', [0 1], 'ylim', [0 1], 'zdir', 'reverse');
 
 box on;
-axis equal
-title('MMC fluence rate (W/cm^2) per W simulated')
+axis equal;
+title('MMC fluence rate (W/cm^2) per W simulated');
 colorbar;
-colormap(jet)
+colormap(jet);
diff --git a/mmclab/example/demo_mmcl_b1_b1d.m b/mmclab/example/demo_mmcl_b1_b1d.m
index 176adebb..26e5c3a1 100644
--- a/mmclab/example/demo_mmcl_b1_b1d.m
+++ b/mmclab/example/demo_mmcl_b1_b1d.m
@@ -1,7 +1,7 @@
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% validate MMC with a homogeneous cubic domain
 %  (see MMC paper Fig. 2 and MMCL paper Fig. 1a)
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %
 % In this example, we validate the MMCM algorithm using a homogeneous
 % cubic domain. This simulation generates the results
@@ -13,95 +13,93 @@
 % tddiffusion (for time-domain solutions) functions in the
 % package of Monte Carlo eXtreme (MCX) under the mcx/utils directory.
 %
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-%addpath('/Please/add/path/to/mcx/utils/')
+% addpath('/Please/add/path/to/mcx/utils/')
 addpath('../../matlab/');
 
-clear cfg
-cfg.nphoton=1e6;
-cfg.seed=1648335518;
-[cfg.node,cfg.elem]=genT5mesh(0:2:60,0:2:60,0:2:60);
-cfg.elemprop=ones(size(cfg.elem,1),1);
-cfg.srcpos=[30.1,30.2,0];
-cfg.srcdir=[0 0 1];
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=1e-10;
-cfg.prop=[0 0 1 1;0.005 1.0 0.01 1.0];
-cfg.debuglevel='TP';
-cfg.isreflect=0;
-cfg.method='elem';
-
-cfg.gpuid=1;
-
-b1gpu=mmclab(cfg);
-b1gpu=sum(b1gpu.data,2);
+clear cfg;
+cfg.nphoton = 1e6;
+cfg.seed = 1648335518;
+[cfg.node, cfg.elem] = genT5mesh(0:2:60, 0:2:60, 0:2:60);
+cfg.elemprop = ones(size(cfg.elem, 1), 1);
+cfg.srcpos = [30.1, 30.2, 0];
+cfg.srcdir = [0 0 1];
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 1e-10;
+cfg.prop = [0 0 1 1; 0.005 1.0 0.01 1.0];
+cfg.debuglevel = 'TP';
+cfg.isreflect = 0;
+cfg.method = 'elem';
+
+cfg.gpuid = 1;
+
+b1gpu = mmclab(cfg);
+b1gpu = sum(b1gpu.data, 2);
 
 %%
-cfg.gpuid=-1;
+cfg.gpuid = -1;
 
-b1cpu=mmclab(cfg);
-b1cpu=sum(b1cpu.data,2);
+b1cpu = mmclab(cfg);
+b1cpu = sum(b1cpu.data, 2);
 
-
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% add paths to the necessary toolboxes
-%%-----------------------------------------------------------------
-
-c0=299792458000;
+%% -----------------------------------------------------------------
 
-twin=[cfg.tstart+cfg.tstep/2:cfg.tstep:cfg.tend];
-gates=length(twin);
+c0 = 299792458000;
 
-[xi,yi]=meshgrid(0.5:1:59.5,0.5:1:59.5);
+twin = [cfg.tstart + cfg.tstep / 2:cfg.tstep:cfg.tend];
+gates = length(twin);
 
-[cutpos1,cutvalue1,facedata1]=qmeshcut(cfg.elem(:,1:4),cfg.node,b1cpu,[0 30.5 0; 0 30.5 1; 1 30.5 0]);
-[cutpos2,cutvalue2,facedata2]=qmeshcut(cfg.elem(:,1:4),cfg.node,b1gpu,[0 30.5 0; 0 30.5 1; 1 30.5 0]);
-Phicpu=griddata(cutpos1(:,1),cutpos1(:,3),cutvalue1,xi,yi);
-Phigpu=griddata(cutpos2(:,1),cutpos2(:,3),cutvalue2,xi,yi);
+[xi, yi] = meshgrid(0.5:1:59.5, 0.5:1:59.5);
 
+[cutpos1, cutvalue1, facedata1] = qmeshcut(cfg.elem(:, 1:4), cfg.node, b1cpu, [0 30.5 0; 0 30.5 1; 1 30.5 0]);
+[cutpos2, cutvalue2, facedata2] = qmeshcut(cfg.elem(:, 1:4), cfg.node, b1gpu, [0 30.5 0; 0 30.5 1; 1 30.5 0]);
+Phicpu = griddata(cutpos1(:, 1), cutpos1(:, 3), cutvalue1, xi, yi);
+Phigpu = griddata(cutpos2(:, 1), cutpos2(:, 3), cutvalue2, xi, yi);
 
 %% DMMC
 
-[cfg.node,cfg.elem]=meshgrid6(0:60:60,0:60:60,0:60:60);
-cfg.elem(:,1:4)=meshreorient(cfg.node,cfg.elem(:,1:4));
+[cfg.node, cfg.elem] = meshgrid6(0:60:60, 0:60:60, 0:60:60);
+cfg.elem(:, 1:4) = meshreorient(cfg.node, cfg.elem(:, 1:4));
 
-cfg.elemprop=ones(size(cfg.elem,1),1);
-cfg.method='grid';
+cfg.elemprop = ones(size(cfg.elem, 1), 1);
+cfg.method = 'grid';
 
-cfg.gpuid=1;
+cfg.gpuid = 1;
 
-flux=mmclab(cfg);
+flux = mmclab(cfg);
 
-Phidgpu=sum(flux.data,4);
+Phidgpu = sum(flux.data, 4);
 
-%% DMMC 
-cfg.gpuid=-1;
+%% DMMC
+cfg.gpuid = -1;
 
-flux=mmclab(cfg);
-Phidcpu=sum(flux.data,4);
+flux = mmclab(cfg);
+Phidcpu = sum(flux.data, 4);
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% generate a contour plot along y=30.5
-%%-----------------------------------------------------------------
-figure
+%% -----------------------------------------------------------------
+figure;
 clines = 0:-0.5:-8;
-[xi,yi]=meshgrid(0.5:1:59.5,0.5:1:59.5);
-srcs=[30.1,30.2,0];
-dets=[xi(:) 30.2*ones(size(xi(:))) yi(:)];
-
-hold on
-[c h2]=contourf(xi,yi, log10(max(squeeze(Phicpu*cfg.tstep),1e-8)), clines, 'k-', 'linewidth', 2);
-contour(xi,yi,log10(abs(Phigpu*cfg.tstep)),clines,'g--','linewidth',2)
-contour(xi,yi,log10(abs(squeeze(Phidcpu(1:end-1,31,1:end-1))'*cfg.tstep)),clines,'b--','linewidth',2)
-contour(xi,yi,log10(abs(squeeze(Phidgpu(1:end-1,31,1:end-1))'*cfg.tstep)),clines,'r-','linewidth',1)
-
-axis equal  
-set(gca,'xlim',[0.5 59.5])
-set(gca,'fontsize',20)
-xlabel('x (mm)')
-ylabel('z (mm)')
-legend('B1-MMC','B1-MMCL','B1D-MMC','B1D-MMCL')
+[xi, yi] = meshgrid(0.5:1:59.5, 0.5:1:59.5);
+srcs = [30.1, 30.2, 0];
+dets = [xi(:) 30.2 * ones(size(xi(:))) yi(:)];
+
+hold on;
+[c h2] = contourf(xi, yi, log10(max(squeeze(Phicpu * cfg.tstep), 1e-8)), clines, 'k-', 'linewidth', 2);
+contour(xi, yi, log10(abs(Phigpu * cfg.tstep)), clines, 'g--', 'linewidth', 2);
+contour(xi, yi, log10(abs(squeeze(Phidcpu(1:end - 1, 31, 1:end - 1))' * cfg.tstep)), clines, 'b--', 'linewidth', 2);
+contour(xi, yi, log10(abs(squeeze(Phidgpu(1:end - 1, 31, 1:end - 1))' * cfg.tstep)), clines, 'r-', 'linewidth', 1);
+
+axis equal;
+set(gca, 'xlim', [0.5 59.5]);
+set(gca, 'fontsize', 20);
+xlabel('x (mm)');
+ylabel('z (mm)');
+legend('B1-MMC', 'B1-MMCL', 'B1D-MMC', 'B1D-MMCL');
 legend boxoff;
 box on;
diff --git a/mmclab/example/demo_mmcl_b2_b2d.m b/mmclab/example/demo_mmcl_b2_b2d.m
index dda287a0..3c9aa06c 100644
--- a/mmclab/example/demo_mmcl_b2_b2d.m
+++ b/mmclab/example/demo_mmcl_b2_b2d.m
@@ -1,173 +1,173 @@
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% validate DMMC with MMC in a heterogeneous cubic domain
 %  (see DMMC paper Fig. 1, and MMCL paper Fig. 1b)
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
 % create a surface mesh for a 10 mm radius sphere
-[nsph_10,fsph_10]=meshasphere([30 30 30],10,1.0);
-[nsph_10,fsph_10]=removeisolatednode(nsph_10,fsph_10);
+[nsph_10, fsph_10] = meshasphere([30 30 30], 10, 1.0);
+[nsph_10, fsph_10] = removeisolatednode(nsph_10, fsph_10);
 
 % create a surface mesh for a 23 mm radius sphere
-[nsph_23,fsph_23]=meshasphere([30 30 30],23,2.0);
-[nsph_23,fsph_23]=removeisolatednode(nsph_23,fsph_23);
+[nsph_23, fsph_23] = meshasphere([30 30 30], 23, 2.0);
+[nsph_23, fsph_23] = removeisolatednode(nsph_23, fsph_23);
 
 % create a surface mesh for a 25 mm radius sphere
-[nsph_25,fsph_25]=meshasphere([30 30 30],25,2.0);
-[nsph_25,fsph_25]=removeisolatednode(nsph_25,fsph_25);
+[nsph_25, fsph_25] = meshasphere([30 30 30], 25, 2.0);
+[nsph_25, fsph_25] = removeisolatednode(nsph_25, fsph_25);
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% create simulation parameters
-%%-----------------------------------------------------------------
-clear cfg
-
-cfg.nphoton=1e8;
-cfg.seed=1648335518;
-cfg.srcpos=[30,30.1,0];
-cfg.srcdir=[0 0 1];
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=5e-10;
-cfg.prop=[0,0,1,1;0.02 7.0 0.89 1.37;0.004 0.009 0.89 1.37;0.02 9.0 0.89 1.37;0.05 0.0 1.0 1.37];
-cfg.debuglevel='TP';
-cfg.isreflect=1;
-
-cfgs=[cfg cfg];
-
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
+clear cfg;
+
+cfg.nphoton = 1e8;
+cfg.seed = 1648335518;
+cfg.srcpos = [30, 30.1, 0];
+cfg.srcdir = [0 0 1];
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 5e-10;
+cfg.prop = [0, 0, 1, 1; 0.02 7.0 0.89 1.37; 0.004 0.009 0.89 1.37; 0.02 9.0 0.89 1.37; 0.05 0.0 1.0 1.37];
+cfg.debuglevel = 'TP';
+cfg.isreflect = 1;
+
+cfgs = [cfg cfg];
+
+%% -----------------------------------------------------------------
 %% tetrahedral mesh generation
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
-% generate a coarse CDT volumetric mesh from triangular surfaces of 
+% generate a coarse CDT volumetric mesh from triangular surfaces of
 % three spheres with an additional bounding box for DMMC
 
-ISO2MESH_SESSION='dmmc1_';
+ISO2MESH_SESSION = 'dmmc1_';
 
-[nbox,ebox]=meshgrid6(0:60:60,0:60:60,0:60:60);
-fbox=volface(ebox);
-[no,fc]=mergemesh(nsph_10,fsph_10,nsph_23,fsph_23,nsph_25,fsph_25,nbox,fbox);
-[no,fc]=removeisolatednode(no,fc);
+[nbox, ebox] = meshgrid6(0:60:60, 0:60:60, 0:60:60);
+fbox = volface(ebox);
+[no, fc] = mergemesh(nsph_10, fsph_10, nsph_23, fsph_23, nsph_25, fsph_25, nbox, fbox);
+[no, fc] = removeisolatednode(no, fc);
 
-ISO2MESH_TETGENOPT='-A -q -Y'
-[cfgs(1).node,cfgs(1).elem]=surf2mesh(no,fc,[0 0 0],[60.1 60.1 60.1],1,100,[1 1 1;30 30 6;30 30 15;30 30 30]);%thin layer
+ISO2MESH_TETGENOPT = '-A -q -Y';
+[cfgs(1).node, cfgs(1).elem] = surf2mesh(no, fc, [0 0 0], [60.1 60.1 60.1], 1, 100, [1 1 1; 30 30 6; 30 30 15; 30 30 30]); % thin layer
 % [cfgs(1).node,cfgs(1).elem]=surf2mesh(no,fc,[0 0 0],[60.1 60.1 60.1],1,100,[1 1 1;30 30 6;30 30 17;30 30 30]);%thick layer
-cfgs(1).method='grid';
+cfgs(1).method = 'grid';
 
-% generate a refined volumetric mesh from triangular surfaces of 
+% generate a refined volumetric mesh from triangular surfaces of
 % three spheres with an additional bounding box for MMC
-clear ISO2MESH_TETGENOPT
-ISO2MESH_SESSION='dmmc2_';
+clear ISO2MESH_TETGENOPT;
+ISO2MESH_SESSION = 'dmmc2_';
 
-[no,fc]=mergemesh(nsph_10,fsph_10,nsph_23,fsph_23,nsph_25,fsph_25);
-[no,fc]=removeisolatednode(no,fc);
-srcpos=cfgs(1).srcpos;
-[cfgs(2).node,cfgs(2).elem,face2]=surf2mesh(no,fc,[0 0 0],[60 60 60],1,0.25,[1 1 1 0.1;30 30 6 0.1;30 30 17 0.1;30 30 30 0.1],[],[1 1 1 1 1 1 1 1]);
-[cfgs(2).node,cfgs(2).elem]=sortmesh(srcpos,cfgs(2).node,cfgs(2).elem,1:4);
-cfgs(2).method='elem';
+[no, fc] = mergemesh(nsph_10, fsph_10, nsph_23, fsph_23, nsph_25, fsph_25);
+[no, fc] = removeisolatednode(no, fc);
+srcpos = cfgs(1).srcpos;
+[cfgs(2).node, cfgs(2).elem, face2] = surf2mesh(no, fc, [0 0 0], [60 60 60], 1, 0.25, [1 1 1 0.1; 30 30 6 0.1; 30 30 17 0.1; 30 30 30 0.1], [], [1 1 1 1 1 1 1 1]);
+[cfgs(2).node, cfgs(2).elem] = sortmesh(srcpos, cfgs(2).node, cfgs(2).elem, 1:4);
+cfgs(2).method = 'elem';
 
 %%
 
-cfgs(1).gpuid=1;
-b2dgpu=mmclab(cfgs(1));
-b2dgpu=sum(b2dgpu.data,4);
+cfgs(1).gpuid = 1;
+b2dgpu = mmclab(cfgs(1));
+b2dgpu = sum(b2dgpu.data, 4);
 
 %%
-cfgs(1).gpuid=-1;
-b2dcpu=mmclab(cfgs(1));
-b2dcpu=sum(b2dcpu.data,4);
+cfgs(1).gpuid = -1;
+b2dcpu = mmclab(cfgs(1));
+b2dcpu = sum(b2dcpu.data, 4);
 
 %%
-cfgs(2).gpuid=1;
-b2gpu=mmclab(cfgs(2));
-b2gpu=sum(b2gpu.data,2);
+cfgs(2).gpuid = 1;
+b2gpu = mmclab(cfgs(2));
+b2gpu = sum(b2gpu.data, 2);
 
 %%
-cfgs(2).gpuid=-1;
-b2cpu=mmclab(cfgs(2));
-b2cpu=sum(b2cpu.data,2);
+cfgs(2).gpuid = -1;
+b2cpu = mmclab(cfgs(2));
+b2cpu = sum(b2cpu.data, 2);
 
-%% 
-[xi,yi]=meshgrid(0.5:59.5,0.5:59.5);
-[cutpos1,cutvalue1,facedata1]=qmeshcut(cfgs(2).elem(:,1:4),cfgs(2).node,b2cpu,[0 30.5 0; 0 30.5 1; 1 30.5 0]);
-[cutpos2,cutvalue2,facedata2]=qmeshcut(cfgs(2).elem(:,1:4),cfgs(2).node,b2gpu,[0 30.5 0; 0 30.5 1; 1 30.5 0]);
-b2cpu_interpolated=griddata(cutpos1(:,1),cutpos1(:,3),cutvalue1,xi,yi);
-b2gpu_interpolated=griddata(cutpos2(:,1),cutpos2(:,3),cutvalue2,xi,yi);
+%%
+[xi, yi] = meshgrid(0.5:59.5, 0.5:59.5);
+[cutpos1, cutvalue1, facedata1] = qmeshcut(cfgs(2).elem(:, 1:4), cfgs(2).node, b2cpu, [0 30.5 0; 0 30.5 1; 1 30.5 0]);
+[cutpos2, cutvalue2, facedata2] = qmeshcut(cfgs(2).elem(:, 1:4), cfgs(2).node, b2gpu, [0 30.5 0; 0 30.5 1; 1 30.5 0]);
+b2cpu_interpolated = griddata(cutpos1(:, 1), cutpos1(:, 3), cutvalue1, xi, yi);
+b2gpu_interpolated = griddata(cutpos2(:, 1), cutpos2(:, 3), cutvalue2, xi, yi);
 
 %% mcxcl - add voxelated mcxcl results
 
-cfg_mcx.nphoton=cfgs(1).nphoton;
+cfg_mcx.nphoton = cfgs(1).nphoton;
 
 % define three spheres with radius=10 mm, 23 mm and 25 mm within a 60x60x60 mm box
-dim=60;
-[xi,yi,zi]=meshgrid(0.5:(dim-0.5),0.5:(dim-0.5),0.5:(dim-0.5));
-dist=(xi-30).^2+(yi-30).^2+(zi-30).^2;
-cfg_mcx.vol=ones(size(xi));
-cfg_mcx.vol(dist<625)=2;%radius 25
-cfg_mcx.vol(dist<529)=3;%radius 23
-cfg_mcx.vol(dist<100)=4;%radius 10
-cfg_mcx.vol=uint8(cfg_mcx.vol);
+dim = 60;
+[xi, yi, zi] = meshgrid(0.5:(dim - 0.5), 0.5:(dim - 0.5), 0.5:(dim - 0.5));
+dist = (xi - 30).^2 + (yi - 30).^2 + (zi - 30).^2;
+cfg_mcx.vol = ones(size(xi));
+cfg_mcx.vol(dist < 625) = 2; % radius 25
+cfg_mcx.vol(dist < 529) = 3; % radius 23
+cfg_mcx.vol(dist < 100) = 4; % radius 10
+cfg_mcx.vol = uint8(cfg_mcx.vol);
 
 % define the source position
-cfg_mcx.srcpos=[30,30.1,0];
-cfg_mcx.srcdir=[0 0 1];
-cfg_mcx.issrcfrom0=1;
+cfg_mcx.srcpos = [30, 30.1, 0];
+cfg_mcx.srcdir = [0 0 1];
+cfg_mcx.issrcfrom0 = 1;
 
 % format: [mua(1/mm) mus(1/mm) g n]
-cfg_mcx.prop=[0,0,1,1;0.02 7.0 0.89 1.37;0.004 0.009 0.89 1.37;0.02 9.0 0.89 1.37;0.05 0.0 1.0 1.37];
+cfg_mcx.prop = [0, 0, 1, 1; 0.02 7.0 0.89 1.37; 0.004 0.009 0.89 1.37; 0.02 9.0 0.89 1.37; 0.05 0.0 1.0 1.37];
 
 % time-domain simulation parameters
-cfg_mcx.tstart=0;
-cfg_mcx.tend=5e-9;
-cfg_mcx.tstep=5e-10;
-  
+cfg_mcx.tstart = 0;
+cfg_mcx.tend = 5e-9;
+cfg_mcx.tstep = 5e-10;
+
 % GPU thread configuration
-cfg_mcx.autopilot=1;
-cfg_mcx.gpuid=1;
+cfg_mcx.autopilot = 1;
+cfg_mcx.gpuid = 1;
 
-cfg_mcx.isreflect=1; % disable reflection at exterior boundaries
-cfg_mcx.unitinmm=1; % resolution
+cfg_mcx.isreflect = 1; % disable reflection at exterior boundaries
+cfg_mcx.unitinmm = 1; % resolution
 
-phimcx=mcxlabcl(cfg_mcx);
-b2mcx=sum(phimcx.data,4);
+phimcx = mcxlabcl(cfg_mcx);
+b2mcx = sum(phimcx.data, 4);
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% generate a contour plot along y=30.5
-%%-----------------------------------------------------------------
-figure
+%% -----------------------------------------------------------------
+figure;
 clines = 0:-0.5:-8;
-[xi,yi]=meshgrid(0.5:59.5,0.5:59.5);
-srcs=[30.1,30.2,0];
-dets=[xi(:) 30.2*ones(size(xi(:))) yi(:)];
-
-hold on
-[c h2]=contourf(xi,yi, log10(max(squeeze(b2cpu_interpolated*cfgs(1).tstep),1e-8)), clines, 'k-','linewidth', 2 );
-contour(xi,yi,log10(abs(b2gpu_interpolated*cfgs(1).tstep)),clines,'g--','linewidth',2);
-contour(xi,yi,log10(abs(squeeze(b2dcpu(1:end-1,31,1:end-1))'*cfgs(1).tstep)),clines,'b--','linewidth',2)
-contour(xi,yi,log10(abs(squeeze(b2dgpu(1:end-1,31,1:end-1))'*cfgs(1).tstep)),clines,'r-','linewidth',1)
-contour(xi,yi,log10(abs(squeeze(b2mcx(:,31,:))'*cfg_mcx.tstep)),clines,'m--')
-
-%plot a dashed circle with radius of 10
-[xcirc,ycirc] = cylinder(sqrt(10^2-0.5^2),200); %since we are ploting at y=30.5,0.5 from center of the sphere.
-xcirc=xcirc(1,:)+30;
-ycirc=ycirc(1,:)+30;
-plot(xcirc,ycirc,'k--','linewidth',2);
-
-%plot a dashed circle with radius of 23
-[xcirc,ycirc] = cylinder(sqrt(23^2-0.5^2),200);
-xcirc=xcirc(1,:)+30;
-ycirc=ycirc(1,:)+30;
-plot(xcirc,ycirc,'k--','linewidth',2);
-
-%plot a dashed circle with radius of 25
-[xcirc,ycirc] = cylinder(sqrt(25^2-0.5^2),200);
-xcirc=xcirc(1,:)+30;
-ycirc=ycirc(1,:)+30;
-plot(xcirc,ycirc,'k--','linewidth',2);
-
-axis equal  
-set(gca,'xlim',[0.5 59.5])
-set(gca,'fontsize',20)
-xlabel('x (mm)')
-ylabel('z (mm)')
-legend('MMC','MMCL','D-MMC','D-MMCL','MCX-CL')
+[xi, yi] = meshgrid(0.5:59.5, 0.5:59.5);
+srcs = [30.1, 30.2, 0];
+dets = [xi(:) 30.2 * ones(size(xi(:))) yi(:)];
+
+hold on;
+[c h2] = contourf(xi, yi, log10(max(squeeze(b2cpu_interpolated * cfgs(1).tstep), 1e-8)), clines, 'k-', 'linewidth', 2);
+contour(xi, yi, log10(abs(b2gpu_interpolated * cfgs(1).tstep)), clines, 'g--', 'linewidth', 2);
+contour(xi, yi, log10(abs(squeeze(b2dcpu(1:end - 1, 31, 1:end - 1))' * cfgs(1).tstep)), clines, 'b--', 'linewidth', 2);
+contour(xi, yi, log10(abs(squeeze(b2dgpu(1:end - 1, 31, 1:end - 1))' * cfgs(1).tstep)), clines, 'r-', 'linewidth', 1);
+contour(xi, yi, log10(abs(squeeze(b2mcx(:, 31, :))' * cfg_mcx.tstep)), clines, 'm--');
+
+% plot a dashed circle with radius of 10
+[xcirc, ycirc] = cylinder(sqrt(10^2 - 0.5^2), 200); % since we are ploting at y=30.5,0.5 from center of the sphere.
+xcirc = xcirc(1, :) + 30;
+ycirc = ycirc(1, :) + 30;
+plot(xcirc, ycirc, 'k--', 'linewidth', 2);
+
+% plot a dashed circle with radius of 23
+[xcirc, ycirc] = cylinder(sqrt(23^2 - 0.5^2), 200);
+xcirc = xcirc(1, :) + 30;
+ycirc = ycirc(1, :) + 30;
+plot(xcirc, ycirc, 'k--', 'linewidth', 2);
+
+% plot a dashed circle with radius of 25
+[xcirc, ycirc] = cylinder(sqrt(25^2 - 0.5^2), 200);
+xcirc = xcirc(1, :) + 30;
+ycirc = ycirc(1, :) + 30;
+plot(xcirc, ycirc, 'k--', 'linewidth', 2);
+
+axis equal;
+set(gca, 'xlim', [0.5 59.5]);
+set(gca, 'fontsize', 20);
+xlabel('x (mm)');
+ylabel('z (mm)');
+legend('MMC', 'MMCL', 'D-MMC', 'D-MMCL', 'MCX-CL');
 legend boxoff;
-box on;
\ No newline at end of file
+box on;
diff --git a/mmclab/example/demo_mmcl_b3.m b/mmclab/example/demo_mmcl_b3.m
index 045fd924..81fcfc52 100644
--- a/mmclab/example/demo_mmcl_b3.m
+++ b/mmclab/example/demo_mmcl_b3.m
@@ -1,107 +1,113 @@
-addpath('../../../matlab/'); 
-
-if(~exist('MMC_Collins_Atlas_Mesh_Version_2L.mat','file'))
-     if(~exist('MMC_Collins_Atlas_Mesh_Version_2L.tar.gz','file'))
-          urlwrite('http://downloads.sourceforge.net/project/mcx/mmc/AdultBrain%20Atlas%20FEM%20Mesh/Version%202/MMC_Collins_Atlas_Mesh_Version_2L.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fmcx%2Ffiles%2Fmmc%2FAdultBrain%2520Atlas%2520FEM%2520Mesh%2FVersion%25202%2F&ts=1451344236&use_mirror=tcpdiag','MMC_Collins_Atlas_Mesh_Version_2L.tar.gz');
-     end
-     if(~exist('MMC_Collins_Atlas_Mesh_Version_2L.tar','file'))
-          gunzip('MMC_Collins_Atlas_Mesh_Version_2L.tar.gz');
-     end
-     if(~exist('MMC_Collins_Atlas_Mesh_Version_2L.mat','file'))
-          untar('MMC_Collins_Atlas_Mesh_Version_2L.tar');
-     end
+addpath('../../../matlab/');
+
+if (~exist('MMC_Collins_Atlas_Mesh_Version_2L.mat', 'file'))
+    if (~exist('MMC_Collins_Atlas_Mesh_Version_2L.tar.gz', 'file'))
+        urlwrite('http://downloads.sourceforge.net/project/mcx/mmc/AdultBrain%20Atlas%20FEM%20Mesh/Version%202/MMC_Collins_Atlas_Mesh_Version_2L.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fmcx%2Ffiles%2Fmmc%2FAdultBrain%2520Atlas%2520FEM%2520Mesh%2FVersion%25202%2F&ts=1451344236&use_mirror=tcpdiag', 'MMC_Collins_Atlas_Mesh_Version_2L.tar.gz');
+    end
+    if (~exist('MMC_Collins_Atlas_Mesh_Version_2L.tar', 'file'))
+        gunzip('MMC_Collins_Atlas_Mesh_Version_2L.tar.gz');
+    end
+    if (~exist('MMC_Collins_Atlas_Mesh_Version_2L.mat', 'file'))
+        untar('MMC_Collins_Atlas_Mesh_Version_2L.tar');
+    end
 end
 
-load MMC_Collins_Atlas_Mesh_Version_2L.mat
+load MMC_Collins_Atlas_Mesh_Version_2L.mat;
 
-clear cfg
-cfg.node=node;
-cfg.elem=elem(:,1:4);
-cfg.elemprop=elem(:,5);
+clear cfg;
+cfg.node = node;
+cfg.elem = elem(:, 1:4);
+cfg.elemprop = elem(:, 5);
 
-cfg.tstart=0;
-cfg.tend=5e-09;
-cfg.tstep=2e-10;
+cfg.tstart = 0;
+cfg.tend = 5e-09;
+cfg.tstep = 2e-10;
 
-cfg.srcpos=[75 67.38 167.5];
-cfg.srcdir=[0.1636 0.4569 -0.8743];
-cfg.srcdir=cfg.srcdir/norm(cfg.srcdir);
+cfg.srcpos = [75 67.38 167.5];
+cfg.srcdir = [0.1636 0.4569 -0.8743];
+cfg.srcdir = cfg.srcdir / norm(cfg.srcdir);
 
-cfg.detpos=[   75.0000   77.1900  170.3000    3.0000
-   75.0000   89.0000  171.6000    3.0000
-   75.0000   97.6700  172.4000    3.0000
-   75.0000  102.4000  172.0000    3.0000];
+cfg.detpos = [75.0000   77.1900  170.3000    3.0000
+              75.0000   89.0000  171.6000    3.0000
+              75.0000   97.6700  172.4000    3.0000
+              75.0000  102.4000  172.0000    3.0000];
 
-cfg.prop=[         0         0    1.0000    1.0000 % background/air
-    0.0190    7.8182    0.8900    1.3700 % scalp & skull are both labeled using 1
-%     0.0190    7.8182    0.8900    1.3700 % skull
-    0.0040    0.0090    0.8900    1.3700 % csf
-    0.0200    9.0000    0.8900    1.3700 % gray matters
-    0.0800   40.9000    0.8400    1.3700 % white matters
-         0         0    1.0000    1.0000]; % air pockets
+cfg.prop = [0         0    1.0000    1.0000 % background/air
+            0.0190    7.8182    0.8900    1.3700 % scalp & skull are both labeled using 1
+            %     0.0190    7.8182    0.8900    1.3700 % skull
+            0.0040    0.0090    0.8900    1.3700 % csf
+            0.0200    9.0000    0.8900    1.3700 % gray matters
+            0.0800   40.9000    0.8400    1.3700 % white matters
+            0         0    1.0000    1.0000]; % air pockets
 
-cfg.seed=29012392;
-cfg.nphoton=1e8;
-cfg.method='elem';
+cfg.seed = 29012392;
+cfg.nphoton = 1e8;
+cfg.method = 'elem';
 
 %%
-cfg.gpuid=1;
+cfg.gpuid = 1;
 
-b3gpu=mmclab(cfg);
-b3gpu=sum(b3gpu.data,2)*cfg.tstep;
+b3gpu = mmclab(cfg);
+b3gpu = sum(b3gpu.data, 2) * cfg.tstep;
 %%
-cfg.gpuid=-1;
+cfg.gpuid = -1;
 
-b3cpu=mmclab(cfg);
-b3cpu=sum(b3cpu.data,2)*cfg.tstep;
+b3cpu = mmclab(cfg);
+b3cpu = sum(b3cpu.data, 2) * cfg.tstep;
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% generate a contour plot along y=74.5
-%%-----------------------------------------------------------------
-figure
+%% -----------------------------------------------------------------
+figure;
 
 clines = 0:-0.5:-10;
 
-x_min=min(cfg.node(:,1)); x_max=max(cfg.node(:,1)); bb_size(1,1)=floor(x_max-x_min);
-y_min=min(cfg.node(:,2)); y_max=max(cfg.node(:,2)); bb_size(1,2)=floor(y_max-y_min);
-z_min=min(cfg.node(:,3)); z_max=max(cfg.node(:,3)); bb_size(1,3)=floor(z_max-z_min);
-[yi,zi]=ndgrid((y_min+0.5):(y_min+0.5+bb_size(1,2)-1),(z_min+0.5):(z_min+0.5+bb_size(1,3)-1));
-
-[cutpos1,cutvalue1,facedata1]=qmeshcut(elem(:,1:4),node,b3cpu,[74.5 0 0;74.5 0 1;74.5 1 0]);
-[cutpos2,cutvalue2,facedata2]=qmeshcut(elem(:,1:4),node,b3gpu,[74.5 0 0;74.5 0 1;74.5 1 0]);
-b3cpu_interpolated=griddata(cutpos1(:,2),cutpos1(:,3),cutvalue1,yi,zi);
-b3gpu_interpolated=griddata(cutpos2(:,2),cutpos2(:,3),cutvalue2,yi,zi);
-
-b3cpu_interpolated(find(b3cpu_interpolated==0))=nan;
-b3gpu_interpolated(find(b3gpu_interpolated==0))=nan;
-
-hold on
-contourf(yi,zi,log10(b3cpu_interpolated),clines,'k-','linewidth',2);
-contour(yi,zi,log10(b3gpu_interpolated),clines,'g--','linewidth',2)
-
-x_cut=75-0.5;
-plane=[x_cut 0 0;x_cut 0 1;x_cut 1 0];
-[cutpos,cutvalue,cutedges]=qmeshcut(face(:,1:3),node,node(:,1),plane);
-[cutpos,cutedges]=removedupnodes(cutpos,cutedges);
-cutloop=extractloops(cutedges);
-[nanidx]=find(isnan(cutloop));
-
-for i=1:size(nanidx,2)
-    if(i==1)
-        plot(cutpos(cutloop(1:(nanidx(i)-1)),2),cutpos(cutloop(1:(nanidx(i)-1)),3),'color','k','LineWidth',1.25,'HandleVisibility','off');
-    elseif(i==2)
-        plot(cutpos(cutloop((nanidx(i-1)+1):(nanidx(i)-1)),2),cutpos(cutloop((nanidx(i-1)+1):(nanidx(i)-1)),3),'linestyle','--','color','k','LineWidth',1.25,'HandleVisibility','off');
+x_min = min(cfg.node(:, 1));
+x_max = max(cfg.node(:, 1));
+bb_size(1, 1) = floor(x_max - x_min);
+y_min = min(cfg.node(:, 2));
+y_max = max(cfg.node(:, 2));
+bb_size(1, 2) = floor(y_max - y_min);
+z_min = min(cfg.node(:, 3));
+z_max = max(cfg.node(:, 3));
+bb_size(1, 3) = floor(z_max - z_min);
+[yi, zi] = ndgrid((y_min + 0.5):(y_min + 0.5 + bb_size(1, 2) - 1), (z_min + 0.5):(z_min + 0.5 + bb_size(1, 3) - 1));
+
+[cutpos1, cutvalue1, facedata1] = qmeshcut(elem(:, 1:4), node, b3cpu, [74.5 0 0; 74.5 0 1; 74.5 1 0]);
+[cutpos2, cutvalue2, facedata2] = qmeshcut(elem(:, 1:4), node, b3gpu, [74.5 0 0; 74.5 0 1; 74.5 1 0]);
+b3cpu_interpolated = griddata(cutpos1(:, 2), cutpos1(:, 3), cutvalue1, yi, zi);
+b3gpu_interpolated = griddata(cutpos2(:, 2), cutpos2(:, 3), cutvalue2, yi, zi);
+
+b3cpu_interpolated(find(b3cpu_interpolated == 0)) = nan;
+b3gpu_interpolated(find(b3gpu_interpolated == 0)) = nan;
+
+hold on;
+contourf(yi, zi, log10(b3cpu_interpolated), clines, 'k-', 'linewidth', 2);
+contour(yi, zi, log10(b3gpu_interpolated), clines, 'g--', 'linewidth', 2);
+
+x_cut = 75 - 0.5;
+plane = [x_cut 0 0; x_cut 0 1; x_cut 1 0];
+[cutpos, cutvalue, cutedges] = qmeshcut(face(:, 1:3), node, node(:, 1), plane);
+[cutpos, cutedges] = removedupnodes(cutpos, cutedges);
+cutloop = extractloops(cutedges);
+[nanidx] = find(isnan(cutloop));
+
+for i = 1:size(nanidx, 2)
+    if (i == 1)
+        plot(cutpos(cutloop(1:(nanidx(i) - 1)), 2), cutpos(cutloop(1:(nanidx(i) - 1)), 3), 'color', 'k', 'LineWidth', 1.25, 'HandleVisibility', 'off');
+    elseif (i == 2)
+        plot(cutpos(cutloop((nanidx(i - 1) + 1):(nanidx(i) - 1)), 2), cutpos(cutloop((nanidx(i - 1) + 1):(nanidx(i) - 1)), 3), 'linestyle', '--', 'color', 'k', 'LineWidth', 1.25, 'HandleVisibility', 'off');
     else
-        plot(cutpos(cutloop((nanidx(i-1)+1):(nanidx(i)-1)),2),cutpos(cutloop((nanidx(i-1)+1):(nanidx(i)-1)),3),'linestyle','--','color','k','LineWidth',1.25,'HandleVisibility','off');
+        plot(cutpos(cutloop((nanidx(i - 1) + 1):(nanidx(i) - 1)), 2), cutpos(cutloop((nanidx(i - 1) + 1):(nanidx(i) - 1)), 3), 'linestyle', '--', 'color', 'k', 'LineWidth', 1.25, 'HandleVisibility', 'off');
     end
 end
 
-axis equal  
-set(gca,'xlim',[3 217]);
-set(gca,'ylim',[-1 175]);
-set(gca,'fontsize',20)
-xlabel('x (mm)')
-ylabel('z (mm)')
-legend('MMC','MMCL')
+axis equal;
+set(gca, 'xlim', [3 217]);
+set(gca, 'ylim', [-1 175]);
+set(gca, 'fontsize', 20);
+xlabel('x (mm)');
+ylabel('z (mm)');
+legend('MMC', 'MMCL');
 legend boxoff;
 box on;
diff --git a/mmclab/example/demo_mmcl_b4.m b/mmclab/example/demo_mmcl_b4.m
index 2a960c5b..246e4421 100644
--- a/mmclab/example/demo_mmcl_b4.m
+++ b/mmclab/example/demo_mmcl_b4.m
@@ -1,78 +1,77 @@
 %% create the skin-vessel benchmark mesh
-[no,fc]=latticegrid([0 200],[0 200],[20 32 200]); % create a 3-layer tissue
-no(end,:)=no(end,:);
+[no, fc] = latticegrid([0 200], [0 200], [20 32 200]); % create a 3-layer tissue
+no(end, :) = no(end, :);
 
-fc2=cell2mat(fc);
-fc=[fc2(:,[1 2 3]); fc2(:,[1 3 4])];
+fc2 = cell2mat(fc);
+fc = [fc2(:, [1 2 3]); fc2(:, [1 3 4])];
 
-[ncy,fcy]=meshacylinder([-1,99.5,99.5],[201,99.5,99.5],20,5); % add the vessel
-[newnode,newelem]=surfboolean(no,fc,'first',ncy,fcy);  % merge the two domains
+[ncy, fcy] = meshacylinder([-1, 99.5, 99.5], [201, 99.5, 99.5], 20, 5); % add the vessel
+[newnode, newelem] = surfboolean(no, fc, 'first', ncy, fcy);  % merge the two domains
 
-c0=[10,100,150,26]';
-seeds=[ones(4,2)*100, c0];  % define the regions by index
+c0 = [10, 100, 150, 26]';
+seeds = [ones(4, 2) * 100, c0];  % define the regions by index
 
-[cfg_mmc.node,cfg_mmc.elem]=s2m(newnode,newelem(:,1:3),1,4,'tetgen',seeds,[]); % creating the merged mesh domain
+[cfg_mmc.node, cfg_mmc.elem] = s2m(newnode, newelem(:, 1:3), 1, 4, 'tetgen', seeds, []); % creating the merged mesh domain
 
-voxellen=0.005;
-cfg_mmc.node=cfg_mmc.node*voxellen;
-cfg_mmc.method='elem';
+voxellen = 0.005;
+cfg_mmc.node = cfg_mmc.node * voxellen;
+cfg_mmc.method = 'elem';
 
-figure; 
+figure;
 subplot(121);
-plotmesh(cfg_mmc.node,cfg_mmc.elem);
+plotmesh(cfg_mmc.node, cfg_mmc.elem);
 
-cfg_mmc.elemprop=cfg_mmc.elem(:,5);
-cfg_mmc.elem=cfg_mmc.elem(:,1:4);
+cfg_mmc.elemprop = cfg_mmc.elem(:, 5);
+cfg_mmc.elem = cfg_mmc.elem(:, 1:4);
 
 %% define other properties
 
-cfg_mmc.prop=[0.0000         0.0    1.0000    1
-    3.5640e-05    1.0000    1.0000    1.3700
-   23.0543    9.3985    0.9000    1.3700
-    0.0458   35.6541    0.9000    1.3700
-    1.6572   37.5940    0.9000    1.3700];
+cfg_mmc.prop = [0.0000         0.0    1.0000    1
+                3.5640e-05    1.0000    1.0000    1.3700
+                23.0543    9.3985    0.9000    1.3700
+                0.0458   35.6541    0.9000    1.3700
+                1.6572   37.5940    0.9000    1.3700];
 
-cfg_mmc.srcpos=[100 100 -3]*voxellen;
-cfg_mmc.srcdir=[0 0 1];
+cfg_mmc.srcpos = [100 100 -3] * voxellen;
+cfg_mmc.srcdir = [0 0 1];
 
-cfg_mmc.tstart=0;
-cfg_mmc.tend=5e-8;
-cfg_mmc.tstep=5e-8;
+cfg_mmc.tstart = 0;
+cfg_mmc.tend = 5e-8;
+cfg_mmc.tstep = 5e-8;
 % cfg.outputtype='energy'; %energy deposition in mmc varys with elem volume
-cfg_mmc.outputtype='flux';
-cfg_mmc.minenergy=0.01;
+cfg_mmc.outputtype = 'flux';
+cfg_mmc.minenergy = 0.01;
 
-cfg_mmc.srctype='disk';
-cfg_mmc.srcparam1=[0.3 0 0 0];
+cfg_mmc.srctype = 'disk';
+cfg_mmc.srcparam1 = [0.3 0 0 0];
 
 %% define wide-field disk source by extending the mesh to the widefield src
-srcdef=struct('srctype',cfg_mmc.srctype,'srcpos',cfg_mmc.srcpos,'srcdir',cfg_mmc.srcdir,...
-    'srcparam1',cfg_mmc.srcparam1,'srcparam2',[]);
+srcdef = struct('srctype', cfg_mmc.srctype, 'srcpos', cfg_mmc.srcpos, 'srcdir', cfg_mmc.srcdir, ...
+                'srcparam1', cfg_mmc.srcparam1, 'srcparam2', []);
 
-[cfg_mmc.node,cfg_mmc.elem] = mmcaddsrc(cfg_mmc.node,[cfg_mmc.elem cfg_mmc.elemprop],...
-    mmcsrcdomain(srcdef,[min(cfg_mmc.node);max(cfg_mmc.node)]));
+[cfg_mmc.node, cfg_mmc.elem] = mmcaddsrc(cfg_mmc.node, [cfg_mmc.elem cfg_mmc.elemprop], ...
+                                         mmcsrcdomain(srcdef, [min(cfg_mmc.node); max(cfg_mmc.node)]));
 
-
-cfg_mmc.elemprop=cfg_mmc.elem(:,5);
-cfg_mmc.elem=cfg_mmc.elem(:,1:4);
+cfg_mmc.elemprop = cfg_mmc.elem(:, 5);
+cfg_mmc.elem = cfg_mmc.elem(:, 1:4);
 
 %% other simulation information
 
-cfg_mmc.nphoton=1e8;
-cfg_mmc.seed=1648335518;
+cfg_mmc.nphoton = 1e8;
+cfg_mmc.seed = 1648335518;
 
-cfg_mmc.debuglevel='TP';
-cfg_mmc.isreflect=0;
+cfg_mmc.debuglevel = 'TP';
+cfg_mmc.isreflect = 0;
 
 %% saving coarse mesh
-cfg_mmc.gpuid=1;
-output1=mmclab(cfg_mmc);
-b4gpu=output1.data*cfg_mmc.tstep;
+cfg_mmc.gpuid = 1;
+output1 = mmclab(cfg_mmc);
+b4gpu = output1.data * cfg_mmc.tstep;
 
 %% saving coarse mesh
-cfg_mmc.gpuid=-1;
-output2=mmclab(cfg_mmc);
-b4cpu=output2.data*cfg_mmc.tstep;
+cfg_mmc.gpuid = -1;
+output2 = mmclab(cfg_mmc);
+b4cpu = output2.data * cfg_mmc.tstep;
 
 %% regenerate the mesh using fine mesh
 % cfg_dmmc=cfg_mmc;
@@ -80,13 +79,13 @@
 % cfg_dmmc.node=cfg_dmmc.node*voxellen;
 % cfg_dmmc.elemprop=cfg_dmmc.elem(:,5);
 % cfg_dmmc.elem=cfg_dmmc.elem(:,1:4);
-% 
+%
 % cfg_dmmc.method='grid';
 % cfg_dmmc.unitinmm=voxellen;
-% 
+%
 % [cfg_dmmc.node,cfg_dmmc.elem] = mmcaddsrc(cfg_dmmc.node,[cfg_dmmc.elem cfg_dmmc.elemprop],...
 %     mmcsrcdomain(srcdef,[min(cfg_dmmc.node);max(cfg_dmmc.node)]));
-% 
+%
 % cfg_dmmc.elemprop=cfg_dmmc.elem(:,5);
 % cfg_dmmc.elem=cfg_dmmc.elem(:,1:4);
 % %% saving coarse mesh
@@ -94,7 +93,7 @@
 % % cfg_dmmc.gpuid=1;
 % % b4dgpu=mmclab(cfg_dmmc);
 % % b4dgpu=sum(b4dgpu.data,4);
-% 
+%
 % %% saving coarse mesh
 % cfg_dmmc.gpuid=-1;
 % b4dcpu=mmclab(cfg_dmmc);
@@ -104,63 +103,70 @@
 % x_min=min(cfg.node(:,1)); x_max=max(cfg.node(:,1)); bb_size(1,1)=floor(x_max-x_min);
 % y_min=min(cfg.node(:,2)); y_max=max(cfg.node(:,2)); bb_size(1,2)=floor(y_max-y_min);
 % z_min=min(cfg.node(:,3)); z_max=max(cfg.node(:,3)); bb_size(1,3)=floor(z_max-z_min);
-[yi,zi]=ndgrid(0.0025:0.005:0.9975,0.1025:0.005:0.9975);
-[cutpos1,cutvalue1,facedata1]=qmeshcut(cfg_mmc.elem(:,1:4),cfg_mmc.node,b4cpu,[0.4975 0 0;0.4975 0 1;0.4975 1 0]);
-[cutpos2,cutvalue2,facedata2]=qmeshcut(cfg_mmc.elem(:,1:4),cfg_mmc.node,b4gpu,[0.4975 0 0;0.4975 0 1;0.4975 1 0]);
-b4cpu_interpolated=griddata(cutpos1(:,2),cutpos1(:,3),cutvalue1,yi,zi);
-b4gpu_interpolated=griddata(cutpos2(:,2),cutpos2(:,3),cutvalue2,yi,zi);
+[yi, zi] = ndgrid(0.0025:0.005:0.9975, 0.1025:0.005:0.9975);
+[cutpos1, cutvalue1, facedata1] = qmeshcut(cfg_mmc.elem(:, 1:4), cfg_mmc.node, b4cpu, [0.4975 0 0; 0.4975 0 1; 0.4975 1 0]);
+[cutpos2, cutvalue2, facedata2] = qmeshcut(cfg_mmc.elem(:, 1:4), cfg_mmc.node, b4gpu, [0.4975 0 0; 0.4975 0 1; 0.4975 1 0]);
+b4cpu_interpolated = griddata(cutpos1(:, 2), cutpos1(:, 3), cutvalue1, yi, zi);
+b4gpu_interpolated = griddata(cutpos2(:, 2), cutpos2(:, 3), cutvalue2, yi, zi);
 
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% generate a contour plot along y=30.2
-%%-----------------------------------------------------------------
-figure
+%% -----------------------------------------------------------------
+figure;
 clines = -2:0.25:1;
 
-hold on
-[yyy,zzz]=ndgrid(-0.4975:0.005:0.4975,0.1025:0.005:0.9975);
-contourf(yyy,zzz,log10(b4cpu_interpolated),clines,'k-','linewidth',2);colorbar
-contour(yyy,zzz,log10(b4gpu_interpolated),clines,'m:','linecolor',[0.9100    0.4100    0.1700],'linewidth',2);
-
-[xcirc,ycirc] = cylinder(0.1,10);
-xcirc=xcirc(1,:)-0.0025;
-ycirc=ycirc(1,:)+0.4975;
-plot(xcirc,ycirc,'k--','linewidth',2);
-
-x=[-0.5,0.5]; y=[0.16 0.16];
-plot(x,y,'k--','linewidth',2);
-
-%title('fluence \phi [W/mm^2/W.delivered]')
-axis equal  
-xlabel('y (mm)');xlim([-0.5 0.5]);
-ylabel('z (mm)');ylim([0.1 1]);
-axis equal
-%legend('MMC','MMCL')
-set(gca,'fontsize',20);
+hold on;
+[yyy, zzz] = ndgrid(-0.4975:0.005:0.4975, 0.1025:0.005:0.9975);
+contourf(yyy, zzz, log10(b4cpu_interpolated), clines, 'k-', 'linewidth', 2);
+colorbar;
+contour(yyy, zzz, log10(b4gpu_interpolated), clines, 'm:', 'linecolor', [0.9100    0.4100    0.1700], 'linewidth', 2);
+
+[xcirc, ycirc] = cylinder(0.1, 10);
+xcirc = xcirc(1, :) - 0.0025;
+ycirc = ycirc(1, :) + 0.4975;
+plot(xcirc, ycirc, 'k--', 'linewidth', 2);
+
+x = [-0.5, 0.5];
+y = [0.16 0.16];
+plot(x, y, 'k--', 'linewidth', 2);
+
+% title('fluence \phi [W/mm^2/W.delivered]')
+axis equal;
+xlabel('y (mm)');
+xlim([-0.5 0.5]);
+ylabel('z (mm)');
+ylim([0.1 1]);
+axis equal;
+% legend('MMC','MMCL')
+set(gca, 'fontsize', 20);
 legend boxoff;
 box on;
 
 %% in case if you want to be consistant with Dr. Jacques' results, which is in unit: W/cm^2/W
-figure
+figure;
 clines = 0:0.25:3;
-hold on
-[yyy,zzz]=ndgrid(-0.04975:0.0005:0.04975,0.01025:0.0005:0.09975);
-contourf(yyy,zzz,log10(b4cpu_interpolated*100),clines,'k-','linewidth',2);colorbar
-contour(yyy,zzz,log10(b4gpu_interpolated*100),clines,'g--','linewidth',2);
-
-[xcirc,ycirc] = cylinder(0.01,10);
-xcirc=xcirc(1,:)-0.00025;
-ycirc=ycirc(1,:)+0.04975;
-plot(xcirc,ycirc,'k--','linewidth',2);
-
-x=[-0.05,0.05]; y=[0.016 0.016];
-plot(x,y,'k--','linewidth',2);
-
-
-title('fluence \phi [W/cm^2/W.delivered]')
-xlabel('y [cm]');xlim([-0.05 0.05]);
-ylabel('z [cm]');ylim([0.01 0.1]);
-axis equal
-legend('MMC','MMCL')
-set(gca,'fontsize',20);
+hold on;
+[yyy, zzz] = ndgrid(-0.04975:0.0005:0.04975, 0.01025:0.0005:0.09975);
+contourf(yyy, zzz, log10(b4cpu_interpolated * 100), clines, 'k-', 'linewidth', 2);
+colorbar;
+contour(yyy, zzz, log10(b4gpu_interpolated * 100), clines, 'g--', 'linewidth', 2);
+
+[xcirc, ycirc] = cylinder(0.01, 10);
+xcirc = xcirc(1, :) - 0.00025;
+ycirc = ycirc(1, :) + 0.04975;
+plot(xcirc, ycirc, 'k--', 'linewidth', 2);
+
+x = [-0.05, 0.05];
+y = [0.016 0.016];
+plot(x, y, 'k--', 'linewidth', 2);
+
+title('fluence \phi [W/cm^2/W.delivered]');
+xlabel('y [cm]');
+xlim([-0.05 0.05]);
+ylabel('z [cm]');
+ylim([0.01 0.1]);
+axis equal;
+legend('MMC', 'MMCL');
+set(gca, 'fontsize', 20);
 legend boxoff;
-box on;
\ No newline at end of file
+box on;
diff --git a/mmclab/example/demo_mmclab_basic.m b/mmclab/example/demo_mmclab_basic.m
index b0c4237c..70bec5f3 100644
--- a/mmclab/example/demo_mmclab_basic.m
+++ b/mmclab/example/demo_mmclab_basic.m
@@ -8,36 +8,36 @@
 
 % prepare simulation input
 
-clear cfg
-cfg.nphoton=1e6;
-[cfg.node, face, cfg.elem]=meshabox([0 0 0],[60 60 30],6);
-cfg.elemprop=ones(size(cfg.elem,1),1);
-cfg.srcpos=[30 30 0];
-cfg.srcdir=[0 0 1];
-cfg.prop=[0 0 1 1;0.005 1 0 1.37];
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=5e-9;
-cfg.debuglevel='TP';
-cfg.issaveref=1;  % in addition to volumetric fluence, also save surface diffuse reflectance
-cfg.method='elem';
+clear cfg;
+cfg.nphoton = 1e6;
+[cfg.node, face, cfg.elem] = meshabox([0 0 0], [60 60 30], 6);
+cfg.elemprop = ones(size(cfg.elem, 1), 1);
+cfg.srcpos = [30 30 0];
+cfg.srcdir = [0 0 1];
+cfg.prop = [0 0 1 1; 0.005 1 0 1.37];
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 5e-9;
+cfg.debuglevel = 'TP';
+cfg.issaveref = 1;  % in addition to volumetric fluence, also save surface diffuse reflectance
+cfg.method = 'elem';
 
 %% run the simulation
 
-flux=mmclab(cfg);
+flux = mmclab(cfg);
 
 %% plotting the result
 
 % plot the cross-section of the fluence
 subplot(121);
-plotmesh([cfg.node(:,1:3),log10(abs(flux.data(1:size(cfg.node,1))))],cfg.elem,'y=30','facecolor','interp','linestyle','none')
+plotmesh([cfg.node(:, 1:3), log10(abs(flux.data(1:size(cfg.node, 1))))], cfg.elem, 'y=30', 'facecolor', 'interp', 'linestyle', 'none');
 view([0 1 0]);
 colorbar;
 
 % plot the surface diffuse reflectance
-if(isfield(cfg,'issaveref') && cfg.issaveref==1)
+if (isfield(cfg, 'issaveref') && cfg.issaveref == 1)
     subplot(122);
-    faces=faceneighbors(cfg.elem,'rowmajor');
-    hs=plotmesh(cfg.node,faces,'cdata',log10(flux.dref(:,1)),'linestyle','none');
+    faces = faceneighbors(cfg.elem, 'rowmajor');
+    hs = plotmesh(cfg.node, faces, 'cdata', log10(flux.dref(:, 1)), 'linestyle', 'none');
     colorbar;
-end
\ No newline at end of file
+end
diff --git a/mmclab/example/demo_mmclab_slit.m b/mmclab/example/demo_mmclab_slit.m
index bb6c67e2..1282f340 100644
--- a/mmclab/example/demo_mmclab_slit.m
+++ b/mmclab/example/demo_mmclab_slit.m
@@ -8,33 +8,33 @@
 
 % prepare simulation input
 
-cfg.nphoton=1e7;
-[cfg.node face cfg.elem]=meshabox([0 0 0],[60 60 30],6);
-cfg.elemprop=ones(size(cfg.elem,1),1);
-cfg.srcpos=[20 30 -10];
-cfg.srcdir=[0 0.2 sqrt(1-0.04)];
-cfg.prop=[0 0 1 1;0.005 0.1 0 1.37];
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=5e-9;
-cfg.debuglevel='TP';
-cfg.unitinmm=1;
-cfg.method='elem';
-cfg.srctype='slit';
-cfg.srcparam1=[30 0 0 0];
-cfg.srcparam2=[0 0 0 0];
+cfg.nphoton = 1e7;
+[cfg.node face cfg.elem] = meshabox([0 0 0], [60 60 30], 6);
+cfg.elemprop = ones(size(cfg.elem, 1), 1);
+cfg.srcpos = [20 30 -10];
+cfg.srcdir = [0 0.2 sqrt(1 - 0.04)];
+cfg.prop = [0 0 1 1; 0.005 0.1 0 1.37];
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 5e-9;
+cfg.debuglevel = 'TP';
+cfg.unitinmm = 1;
+cfg.method = 'elem';
+cfg.srctype = 'slit';
+cfg.srcparam1 = [30 0 0 0];
+cfg.srcparam2 = [0 0 0 0];
 
 % run the simulation
 
-flux=mmclab(cfg);
+flux = mmclab(cfg);
 
 % plotting the result
 
 % if you have the SVN version of iso2mesh, use the next line to plot:
 % qmeshcut(cfg.elem(:,1:4),cfg.node(:,1:3),log10(abs(flux.data(:))),'y=30','linestyle','none');
 
-plotmesh([cfg.node(:,1:3),log10(abs(flux.data(1:size(cfg.node,1))))],cfg.elem,'x=40','facecolor','interp','linestyle','none')
+plotmesh([cfg.node(:, 1:3), log10(abs(flux.data(1:size(cfg.node, 1))))], cfg.elem, 'x=40', 'facecolor', 'interp', 'linestyle', 'none');
 hold on;
-plotmesh([cfg.node(:,1:3),log10(abs(flux.data(1:size(cfg.node,1))))],cfg.elem,'y=30','facecolor','interp','linestyle','none')
+plotmesh([cfg.node(:, 1:3), log10(abs(flux.data(1:size(cfg.node, 1))))], cfg.elem, 'y=30', 'facecolor', 'interp', 'linestyle', 'none');
 view(3);
 colorbar;
diff --git a/mmclab/example/demo_photon_sharing.m b/mmclab/example/demo_photon_sharing.m
index 6b7ac321..1a85043d 100644
--- a/mmclab/example/demo_photon_sharing.m
+++ b/mmclab/example/demo_photon_sharing.m
@@ -4,72 +4,77 @@
 
 %% prepare simulation input
 
-cfg.nphoton=3e6;
-[cfg.node face cfg.elem]=meshabox([0 0 0],[60 60 20],2, 2);
-cfg.elemprop=ones(size(cfg.elem,1),1);
-cfg.srcpos=[10 10 -2];
-cfg.srcdir=[0 0 1];
-cfg.srctype='pattern';
-cfg.srcparam1=[40.0 0.0 0.0 40];
-cfg.srcparam2=[0.0 40.0 0.0 40];
-cfg.prop=[0 0 1 1;0.01 10 0.9 1.37];
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=1e-10;
-cfg.gpuid=-1;
-cfg.method='elem';
-cfg.debuglevel='TP';
+cfg.nphoton = 3e6;
+[cfg.node face cfg.elem] = meshabox([0 0 0], [60 60 20], 2, 2);
+cfg.elemprop = ones(size(cfg.elem, 1), 1);
+cfg.srcpos = [10 10 -2];
+cfg.srcdir = [0 0 1];
+cfg.srctype = 'pattern';
+cfg.srcparam1 = [40.0 0.0 0.0 40];
+cfg.srcparam2 = [0.0 40.0 0.0 40];
+cfg.prop = [0 0 1 1; 0.01 10 0.9 1.37];
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 1e-10;
+cfg.gpuid = -1;
+cfg.method = 'elem';
+cfg.debuglevel = 'TP';
 
 %% 5 patterns represented by a 3D matrix
 
-pat=zeros(40,40,5);
-pat(:,:,1) = ones(40);  % full field illumination pattern
-pat(1:20,:,2) = 1;      % pattern with left half bright
-pat(:,1:20,3) = 1;      % pattern with top half bright
-pat(11:30,11:30,4) = 1; % pattern with bright square in the middle
-pat(16:25,:,5) = 1;  
-pat(:,16:25,5) = 1;     % pattern with a bright cross
+pat = zeros(40, 40, 5);
+pat(:, :, 1) = ones(40);  % full field illumination pattern
+pat(1:20, :, 2) = 1;      % pattern with left half bright
+pat(:, 1:20, 3) = 1;      % pattern with top half bright
+pat(11:30, 11:30, 4) = 1; % pattern with bright square in the middle
+pat(16:25, :, 5) = 1;
+pat(:, 16:25, 5) = 1;     % pattern with a bright cross
 
 cfg.srcpattern = pat;
 
 %% run the simulation
 
-flux=mmclab(cfg);
+flux = mmclab(cfg);
 
 %% plot results (same as in the mmc example)
 
-[node, ~, elem]=meshabox([0 0 0],[60 60 20],2, 2);
-data = flux.data(:,1:length(node),:);
-cwdata = squeeze(sum(data,3));
+[node, ~, elem] = meshabox([0 0 0], [60 60 20], 2, 2);
+data = flux.data(:, 1:length(node), :);
+cwdata = squeeze(sum(data, 3));
 
 figure();
 
-subplot(1,3,1); title('pattern 1');
-plotmesh([node,(cwdata(1,:))'],elem,'linestyle','none');
-shading interp
-axis off
-view([0,0,-1])
+subplot(1, 3, 1);
+title('pattern 1');
+plotmesh([node, (cwdata(1, :))'], elem, 'linestyle', 'none');
+shading interp;
+axis off;
+view([0, 0, -1]);
 
-subplot(2,3,2); title('pattern 2');
-plotmesh([node,(cwdata(2,:))'],elem,'linestyle','none');
-shading interp
-axis off
-view([0,0,-1])
+subplot(2, 3, 2);
+title('pattern 2');
+plotmesh([node, (cwdata(2, :))'], elem, 'linestyle', 'none');
+shading interp;
+axis off;
+view([0, 0, -1]);
 
-subplot(2,3,3); title('pattern 3');
-plotmesh([node,(cwdata(3,:))'],elem,'linestyle','none');
-shading interp
-axis off
-view([0,0,-1])
+subplot(2, 3, 3);
+title('pattern 3');
+plotmesh([node, (cwdata(3, :))'], elem, 'linestyle', 'none');
+shading interp;
+axis off;
+view([0, 0, -1]);
 
-subplot(2,3,5); title('pattern 4');
-plotmesh([node,(cwdata(4,:))'],elem,'linestyle','none');
-shading interp
-axis off
-view([0,0,-1])
+subplot(2, 3, 5);
+title('pattern 4');
+plotmesh([node, (cwdata(4, :))'], elem, 'linestyle', 'none');
+shading interp;
+axis off;
+view([0, 0, -1]);
 
-subplot(2,3,6); title('pattern 5');
-plotmesh([node,(cwdata(5,:))'],elem,'linestyle','none');
-shading interp
-axis off
-view([0,0,-1])
+subplot(2, 3, 6);
+title('pattern 5');
+plotmesh([node, (cwdata(5, :))'], elem, 'linestyle', 'none');
+shading interp;
+axis off;
+view([0, 0, -1]);
diff --git a/mmclab/example/demo_sfdi_2layer.m b/mmclab/example/demo_sfdi_2layer.m
index 12cf9664..80d4e0b7 100644
--- a/mmclab/example/demo_sfdi_2layer.m
+++ b/mmclab/example/demo_sfdi_2layer.m
@@ -1,6 +1,6 @@
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% Simulating an SFDI source with a 2-layer brain model
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %
 % In this example, we simulate an spatial-frequency domain imaging source
 % using a 2-layer brain model.
@@ -10,89 +10,89 @@
 % and white matters. The sample SFDI covers a 40 x 40 mm area from the top,
 % and has kx=3 with a pi/3 phase offset in the x-direction.
 %
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 
 clear cfg;
 clear all;
 
 %% 2-layer mesh model
 
-layercount=3;
+layercount = 3;
+
+if (layercount == 2)
+    [node, face, c0] = latticegrid([0 60], [0 60], [0 25 30]);
+    c0(:, 4) = [2; 1];   % maximum element size for bottom (label 1) and top (label 2) layers
 
-if(layercount==2)
-    [node,face,c0]=latticegrid([0 60],[0 60],[0 25 30]);
-    c0(:,4)=[2;1];   % maximum element size for bottom (label 1) and top (label 2) layers
-    
     % simulate the optical properties of skull and gray-matter of a human brain model
     % see http://mcx.sourceforge.net/cgi-bin/index.cgi?MMC/Colin27AtlasMesh
-    cfg.prop=[0 0 1 1;0.02 9.0, 0.89 1.37;0.019 7.8 0.89 1.37]; 
+    cfg.prop = [0 0 1 1; 0.02 9.0, 0.89 1.37; 0.019 7.8 0.89 1.37];
 else
-    [node,face,c0]=latticegrid([0 60],[0 60],[0 20 25 30]); % if you like a 3-layer model
-    c0(:,4)=[2;2;1];
-    cfg.prop=[0 0 1 1;0.02 9.0, 0.89 1.37;0.004 0.009, 0.89 1.37;0.019 7.8 0.89 1.37]; 
+    [node, face, c0] = latticegrid([0 60], [0 60], [0 20 25 30]); % if you like a 3-layer model
+    c0(:, 4) = [2; 2; 1];
+    cfg.prop = [0 0 1 1; 0.02 9.0, 0.89 1.37; 0.004 0.009, 0.89 1.37; 0.019 7.8 0.89 1.37];
 end
-[cfg.node,cfg.elem]=surf2mesh(node,face,[],[],1,[],c0);
+[cfg.node, cfg.elem] = surf2mesh(node, face, [], [], 1, [], c0);
 
-figure; 
+figure;
 subplot(121);
-plotmesh(cfg.node,cfg.elem);
-
-cfg.elemprop=cfg.elem(:,5);
-cfg.elem=cfg.elem(:,1:4);
+plotmesh(cfg.node, cfg.elem);
 
+cfg.elemprop = cfg.elem(:, 5);
+cfg.elem = cfg.elem(:, 1:4);
 
 %% add source and retessellate mesh
 
-cfg.srctype='fourier';      % define an SFDI source
-cfg.srcpos=[10 10 35];      % one corner of the illumination area
-kx=3;                       % wave number in the x-dir
-ky=0;                       % wave number in the x-dir
-xphase=pi/3;                % phase offset in the x-dir, must < 2pi
-yphase=0;                   % phase offset in the x-dir, must < 2pi
-cfg.srcparam1=[40 0 0 kx+xphase/(2*pi)];   % kx is k-number in x direction
-cfg.srcparam2=[0 40 0 ky+yphase/(2*pi)];
-cfg.srcdir=[0 0 -1];
+cfg.srctype = 'fourier';      % define an SFDI source
+cfg.srcpos = [10 10 35];      % one corner of the illumination area
+kx = 3;                       % wave number in the x-dir
+ky = 0;                       % wave number in the x-dir
+xphase = pi / 3;                % phase offset in the x-dir, must < 2pi
+yphase = 0;                   % phase offset in the x-dir, must < 2pi
+cfg.srcparam1 = [40 0 0 kx + xphase / (2 * pi)];   % kx is k-number in x direction
+cfg.srcparam2 = [0 40 0 ky + yphase / (2 * pi)];
+cfg.srcdir = [0 0 -1];
 
 %% line 24-31 could possibly be deleted and replaced by built-in one-step command
-srcdef=struct('srctype',cfg.srctype,'srcpos',cfg.srcpos,'srcdir',cfg.srcdir,...
-    'srcparam1',cfg.srcparam1,'srcparam2',cfg.srcparam2);
+srcdef = struct('srctype', cfg.srctype, 'srcpos', cfg.srcpos, 'srcdir', cfg.srcdir, ...
+                'srcparam1', cfg.srcparam1, 'srcparam2', cfg.srcparam2);
 
-[cfg.node,cfg.elem] = mmcaddsrc(cfg.node,[cfg.elem cfg.elemprop],...
-    mmcsrcdomain(srcdef,[min(cfg.node);max(cfg.node)]));
+[cfg.node, cfg.elem] = mmcaddsrc(cfg.node, [cfg.elem cfg.elemprop], ...
+                                 mmcsrcdomain(srcdef, [min(cfg.node); max(cfg.node)]));
 
-cfg.elemprop=cfg.elem(:,5);
-cfg.elem=cfg.elem(:,1:4);
+cfg.elemprop = cfg.elem(:, 5);
+cfg.elem = cfg.elem(:, 1:4);
 
 %% other simulation information
 
-cfg.nphoton=3e6;
-cfg.seed=1648335518;
+cfg.nphoton = 3e6;
+cfg.seed = 1648335518;
 
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=1e-10;
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 1e-10;
 
-cfg.debuglevel='TP';
-cfg.isreflect=1;
-cfg.detpos=[30 30 0 2]; % detector position
-cfg.method='elem';
+cfg.debuglevel = 'TP';
+cfg.isreflect = 1;
+cfg.detpos = [30 30 0 2]; % detector position
+cfg.method = 'elem';
 
 %% mmc simulation
 
-layer=mmclab(cfg);
-%cube=mmclab(cfg,'sse'); % this is faster
-layer=layer.data;
-layercw=sum(layer,2);
+layer = mmclab(cfg);
+% cube=mmclab(cfg,'sse'); % this is faster
+layer = layer.data;
+layercw = sum(layer, 2);
 
 % plot simulated photon profiles
 
 subplot(122);
 hold on;
-qmeshcut(cfg.elem(cfg.elemprop>0,1:4),cfg.node,log10(layercw),'y=30','linestyle','none'); view(3)
-qmeshcut(cfg.elem(cfg.elemprop>0,1:4),cfg.node,log10(layercw),'z=27','linestyle','none'); 
-if(layercount~=2)
-    qmeshcut(cfg.elem(cfg.elemprop>0,1:4),cfg.node,log10(layercw),'z=22','linestyle','none'); 
+qmeshcut(cfg.elem(cfg.elemprop > 0, 1:4), cfg.node, log10(layercw), 'y=30', 'linestyle', 'none');
+view(3);
+qmeshcut(cfg.elem(cfg.elemprop > 0, 1:4), cfg.node, log10(layercw), 'z=27', 'linestyle', 'none');
+if (layercount ~= 2)
+    qmeshcut(cfg.elem(cfg.elemprop > 0, 1:4), cfg.node, log10(layercw), 'z=22', 'linestyle', 'none');
 end
 box on;
-axis equal
+axis equal;
 view(-56, 22);
diff --git a/mmclab/example/demo_wide_det.m b/mmclab/example/demo_wide_det.m
index 80bdbaf0..522d7558 100644
--- a/mmclab/example/demo_wide_det.m
+++ b/mmclab/example/demo_wide_det.m
@@ -1,31 +1,31 @@
 addpath('../../matlab/');
 addpath('..');
 
-clear cfg
-
-[node,face,c0]=latticegrid([0 60],[0 60],[0 5 10]);
-c0(:,4)=[2;3];   % maximum element size for bottom (label 1) and top (label 2) layers
-[node,elem]=surf2mesh(node,face,[],[],1,[],c0);
-
-detdef=struct('srctype','planar','srcpos',[10,10,-1],'srcdir',[0 0 1],...
-                'srcparam1',[40 0 0 40],'srcparam2',[0 40 0 40]);
-            
-[cfg.node,cfg.elem]=mmcadddet(node,elem,detdef);
-cfg.elemprop=cfg.elem(:,5);
-cfg.elem=cfg.elem(:,1:4);
-cfg.prop = [0 0 1 1;
-                0.01 1.0 0.01 1.37
-                0.05 10.0 0.9 1.37];
-    
+clear cfg;
+
+[node, face, c0] = latticegrid([0 60], [0 60], [0 5 10]);
+c0(:, 4) = [2; 3];   % maximum element size for bottom (label 1) and top (label 2) layers
+[node, elem] = surf2mesh(node, face, [], [], 1, [], c0);
+
+detdef = struct('srctype', 'planar', 'srcpos', [10, 10, -1], 'srcdir', [0 0 1], ...
+                'srcparam1', [40 0 0 40], 'srcparam2', [0 40 0 40]);
+
+[cfg.node, cfg.elem] = mmcadddet(node, elem, detdef);
+cfg.elemprop = cfg.elem(:, 5);
+cfg.elem = cfg.elem(:, 1:4);
+cfg.prop = [0 0 1 1
+            0.01 1.0 0.01 1.37
+            0.05 10.0 0.9 1.37];
+
 cfg.srcpos = [25.0 35.0 10.0];
-cfg.e0 = tsearchn(cfg.node,cfg.elem(:,1:4),cfg.srcpos);
+cfg.e0 = tsearchn(cfg.node, cfg.elem(:, 1:4), cfg.srcpos);
 cfg.srcdir = [0, 0, -1];
 
 cfg.srctype = 'pencil';
 cfg.srcparam1 = [0 0 0 0];
 cfg.srcparam2 = [0 0 0 0];
 
-cfg.detpos = [10.0,10.0,-1.0,0];
+cfg.detpos = [10.0, 10.0, -1.0, 0];
 cfg.detparam1 = [40.0 0.0 0.0 40];
 cfg.detparam2 = [0.0 40.0 0.0 40];
 
@@ -38,8 +38,8 @@
 cfg.debuglevel = 'TP';
 cfg.issaveexit = 2;
 
-[flux,detp]=mmclab(cfg);
+[flux, detp] = mmclab(cfg);
 
 figure;
-imagesc(sum(detp.data,3)');
+imagesc(sum(detp.data, 3)');
 axis equal;
diff --git a/mmclab/example/mmclab_selftest_input.m b/mmclab/example/mmclab_selftest_input.m
index 43c786ba..44459170 100644
--- a/mmclab/example/mmclab_selftest_input.m
+++ b/mmclab/example/mmclab_selftest_input.m
@@ -1,38 +1,38 @@
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %% MMClab self-test script
-%%-----------------------------------------------------------------
+%% -----------------------------------------------------------------
 %
 % In this example, we generate various true or false input conditions
-% and test the robustness of the script to these conditions 
+% and test the robustness of the script to these conditions
 %
 
-dat=mmclab();
+dat = mmclab();
 
-cfg=struct();
-dat=mmclab(cfg);
+cfg = struct();
+dat = mmclab(cfg);
 
-[cfg.node face cfg.elem]=meshabox([0 0 0], [10 10 10],1);
-dat=mmclab(cfg);
+[cfg.node face cfg.elem] = meshabox([0 0 0], [10 10 10], 1);
+dat = mmclab(cfg);
 
-cfg.elem(:,5)=1;
-dat=mmclab(cfg);
+cfg.elem(:, 5) = 1;
+dat = mmclab(cfg);
 
-cfg.srcpos=[5 5 0];
-cfg.srcdir=[0 0 1];
-cfg.nphoton=1000;
-cfg.prop=[0 0 1 1;0.1 1 0.2 1.3];
-dat=mmclab(cfg);
+cfg.srcpos = [5 5 0];
+cfg.srcdir = [0 0 1];
+cfg.nphoton = 1000;
+cfg.prop = [0 0 1 1; 0.1 1 0.2 1.3];
+dat = mmclab(cfg);
 
-cfg.tstart=0;
-cfg.tend=1e-9;
-dat=mmclab(cfg);
+cfg.tstart = 0;
+cfg.tend = 1e-9;
+dat = mmclab(cfg);
 
-cfg.tstep=10e-9;
-dat=mmclab(cfg);
+cfg.tstep = 10e-9;
+dat = mmclab(cfg);
 
-cfg.srcpos=[-1 -1 -1];
-dat=mmclab(cfg);
+cfg.srcpos = [-1 -1 -1];
+dat = mmclab(cfg);
 
-cfg.srcparam1=[0 0 0 0];
-cfg.srcparam2=[0 0 0 0];
-dat=mmclab(cfg);
+cfg.srcparam1 = [0 0 0 0];
+cfg.srcparam2 = [0 0 0 0];
+dat = mmclab(cfg);
diff --git a/mmclab/example/test_albedo.m b/mmclab/example/test_albedo.m
index f11b29cd..07a7dafb 100644
--- a/mmclab/example/test_albedo.m
+++ b/mmclab/example/test_albedo.m
@@ -4,107 +4,107 @@
 
 %% testing albedo method
 
-clear cfg newcfg
-
-cfg.nphoton=1e7;
-cfg.seed=-1;
-
-[cfg.node,cfg.elem]=genT6mesh(0:2:60,0:2:60,0:2:60);
-cfg.elemprop=ones(size(cfg.elem,1),1);
-cfg.srcpos=[30.1,30.2,0];
-cfg.srcdir=[0 0 1];
-cfg.tstart=0;
-cfg.tend=5e-9;
-cfg.tstep=5e-9;
-cfg.prop=[0 0 1 1;0.1 1.0 0.0 1.0];
-cfg.debuglevel='TP';
-cfg.isreflect=0;
-cfg.detpos=[30.1 25.2 0. 1.0];
-cfg.issaveexit=1;  % save detected photon exit position and angles
-cfg.issaveseed=1;  % save detected photon seeds to replay later
-cfg.isnormalized=1;
-cfg.method='elem';
+clear cfg newcfg;
+
+cfg.nphoton = 1e7;
+cfg.seed = -1;
+
+[cfg.node, cfg.elem] = genT6mesh(0:2:60, 0:2:60, 0:2:60);
+cfg.elemprop = ones(size(cfg.elem, 1), 1);
+cfg.srcpos = [30.1, 30.2, 0];
+cfg.srcdir = [0 0 1];
+cfg.tstart = 0;
+cfg.tend = 5e-9;
+cfg.tstep = 5e-9;
+cfg.prop = [0 0 1 1; 0.1 1.0 0.0 1.0];
+cfg.debuglevel = 'TP';
+cfg.isreflect = 0;
+cfg.detpos = [30.1 25.2 0. 1.0];
+cfg.issaveexit = 1;  % save detected photon exit position and angles
+cfg.issaveseed = 1;  % save detected photon seeds to replay later
+cfg.isnormalized = 1;
+cfg.method = 'elem';
 
 % albedo method
-cfg.mcmethod=1; 
-newcfg=mmclab(cfg,'prep');  % preprocessing of the mesh to get the missing fields
-[cube1, detp1]=mmclab(newcfg); % initial simulation
+cfg.mcmethod = 1;
+newcfg = mmclab(cfg, 'prep');  % preprocessing of the mesh to get the missing fields
+[cube1, detp1] = mmclab(newcfg); % initial simulation
 
 % mBLL method
-cfg.mcmethod=0; 
-newcfg=mmclab(cfg,'prep');  % preprocessing of the mesh to get the missing fields
-[cube2, detp2]=mmclab(newcfg); % initial simulation
+cfg.mcmethod = 0;
+newcfg = mmclab(cfg, 'prep');  % preprocessing of the mesh to get the missing fields
+[cube2, detp2] = mmclab(newcfg); % initial simulation
 
 %% CW contour comparison
 
 figure(1);
-[xi,yi] = meshgrid(0:60,0:60);
+[xi, yi] = meshgrid(0:60, 0:60);
 slice = 30;
 
 node = cfg.node;
 elem = cfg.elem;
 
-[cutpos,cutvalue,facedata] = qmeshcut(elem(:,1:4),node,cube1.data,[slice 0 0; slice 0 1; slice 1 0]);
-vi=griddata(cutpos(:,2),cutpos(:,3),cutvalue,xi,yi);
+[cutpos, cutvalue, facedata] = qmeshcut(elem(:, 1:4), node, cube1.data, [slice 0 0; slice 0 1; slice 1 0]);
+vi = griddata(cutpos(:, 2), cutpos(:, 3), cutvalue, xi, yi);
 
-[cutpos,cutvalue,facedata] = qmeshcut(elem(:,1:4),node,cube2.data,[slice 0 0; slice 0 1; slice 1 0]);
-vi2=griddata(cutpos(:,2),cutpos(:,3),cutvalue,xi,yi);
+[cutpos, cutvalue, facedata] = qmeshcut(elem(:, 1:4), node, cube2.data, [slice 0 0; slice 0 1; slice 1 0]);
+vi2 = griddata(cutpos(:, 2), cutpos(:, 3), cutvalue, xi, yi);
 
-contour(log10(abs(vi)),[1:0.5:8],'r:','LineWidth',1.5)
-hold on
-contour(log10(abs(vi2)),[1:0.5:8],'b','LineWidth',1.5)
-grid on
+contour(log10(abs(vi)), [1:0.5:8], 'r:', 'LineWidth', 1.5);
+hold on;
+contour(log10(abs(vi2)), [1:0.5:8], 'b', 'LineWidth', 1.5);
+grid on;
 
-xlabel('y(mm)','FontSize',20);
-ylabel('z(mm)','FontSize',20);
-title('plane x=30 mm','FontSize',20);
-set(gca,'FontSize',20);
+xlabel('y(mm)', 'FontSize', 20);
+ylabel('z(mm)', 'FontSize', 20);
+title('plane x=30 mm', 'FontSize', 20);
+set(gca, 'FontSize', 20);
 
-legend('albedo','mBLL');
+legend('albedo', 'mBLL');
 
 %% detected weight comparison CW
 
-mua=0.1;
-mus=1;
-mut=mua+mus;
+mua = 0.1;
+mus = 1;
+mut = mua + mus;
 
-w1 = detp1.w0.*(mus/mut).^double(detp1.nscat);
-w2 = detp2.w0.*exp(-mua*double(detp2.ppath));
+w1 = detp1.w0 .* (mus / mut).^double(detp1.nscat);
+w2 = detp2.w0 .* exp(-mua * double(detp2.ppath));
 
-abs(sum(w1)-sum(w2))/sum(w2)
+abs(sum(w1) - sum(w2)) / sum(w2);
 
 %% detected weight comparison (TD)
 
 c0 = 3e11;
 n = 1;
-cc = c0/n;
+cc = c0 / n;
 
 nTG = 50;
 gate_width = 2e-11;
 
-tpsf1 = zeros(nTG,1);
-tpsf2 = zeros(nTG,1);
+tpsf1 = zeros(nTG, 1);
+tpsf2 = zeros(nTG, 1);
 
 for i = 1:length(detp1.ppath)
-    tg = floor(detp1.ppath(i)/cc/gate_width)+1;
-    tpsf1(tg) = tpsf1(tg)+w1(i);
+    tg = floor(detp1.ppath(i) / cc / gate_width) + 1;
+    tpsf1(tg) = tpsf1(tg) + w1(i);
 end
 
 for i = 1:length(detp2.ppath)
-    tg = floor(detp2.ppath(i)/cc/gate_width)+1;
-    tpsf2(tg) = tpsf2(tg)+w2(i);
+    tg = floor(detp2.ppath(i) / cc / gate_width) + 1;
+    tpsf2(tg) = tpsf2(tg) + w2(i);
 end
 
 %% weighted ppath and nscat comparison
 
 % scattering events
-p1 = sum(double(detp1.nscat).*w1);
-p1_ave = p1/length(detp1.nscat);
-p2 = sum(double(detp2.nscat).*w2);
-p2_ave = p2/length(detp2.nscat);
+p1 = sum(double(detp1.nscat) .* w1);
+p1_ave = p1 / length(detp1.nscat);
+p2 = sum(double(detp2.nscat) .* w2);
+p2_ave = p2 / length(detp2.nscat);
 
 % pathlength
-L1 = sum(double(detp1.ppath).*w1);
-L1_ave = L1/length(detp1.nscat);
-L2 = sum(double(detp2.ppath).*w2);
-L2_ave = L2/length(detp2.nscat);
+L1 = sum(double(detp1.ppath) .* w1);
+L1_ave = L1 / length(detp1.nscat);
+L2 = sum(double(detp2.ppath) .* w2);
+L2_ave = L2 / length(detp2.nscat);
diff --git a/mmclab/mmc2json.m b/mmclab/mmc2json.m
index 1849adb0..6a77a912 100644
--- a/mmclab/mmc2json.m
+++ b/mmclab/mmc2json.m
@@ -1,4 +1,4 @@
-function varargout = mmc2json(cfg,filestub, varargin)
+function varargout = mmc2json(cfg, filestub, varargin)
 %
 % Format:
 %    mmc2json(cfg,filestub)
@@ -8,7 +8,7 @@
 % Author: Qianqian Fang <q.fang at neu.edu>
 %
 % Input:
-%    cfg: a struct defining the parameters associated with a simulation. 
+%    cfg: a struct defining the parameters associated with a simulation.
 %         Please run 'help mcxlab' or 'help mmclab' to see the details.
 %         mcxpreview supports the cfg input for both mcxlab and mmclab.
 %    filestub: the filestub is the name stub for all output files,including
@@ -18,8 +18,8 @@
 %         filestub_pattern.bin: the domain shape file if cfg.pattern is defined
 %
 % Dependency:
-%    this function depends on the savejson/saveubjson functions from the 
-%    Iso2Mesh toolbox (http://iso2mesh.sf.net) or JSONlab toolbox 
+%    this function depends on the savejson/saveubjson functions from the
+%    Iso2Mesh toolbox (http://iso2mesh.sf.net) or JSONlab toolbox
 %    (http://iso2mesh.sf.net/jsonlab)
 %
 % This function is part of Monte Carlo eXtreme (MCX) URL: http://mcx.space
@@ -27,86 +27,86 @@
 % License: GNU General Public License version 3, please read LICENSE.txt for details
 %
 
-singlefile = (nargin ==1 || ~isempty(regexp(filestub,'\.json$', 'once')));
+singlefile = (nargin == 1 || ~isempty(regexp(filestub, '\.json$', 'once')));
 
-if(nargin > 1)
-    [fpath, fname, fext]=fileparts(filestub);
-    filestub=fullfile(fpath,fname);
+if (nargin > 1)
+    [fpath, fname, fext] = fileparts(filestub);
+    filestub = fullfile(fpath, fname);
 end
 
 %% define the optodes: sources and detectors
 
-Optode.Source=struct();
-Optode.Source=copycfg(cfg,'srcpos',Optode.Source,'Pos');
-Optode.Source=copycfg(cfg,'srcdir',Optode.Source,'Dir');
-Optode.Source=copycfg(cfg,'srcparam1',Optode.Source,'Param1');
-Optode.Source=copycfg(cfg,'srcparam2',Optode.Source,'Param2');
-Optode.Source=copycfg(cfg,'srctype',Optode.Source,'Type');
-Optode.Source=copycfg(cfg,'srcnum',Optode.Source,'SrcNum');
-
-if(isfield(cfg,'detpos') && ~isempty(cfg.detpos))
-    Optode.Detector=struct();
-    Optode.Detector=cell2struct(mat2cell(cfg.detpos, ones(1,size(cfg.detpos,1)),[3 1]), {'Pos','R'} ,2);
-    if(length(Optode.Detector)==1)
-        Optode.Detector={Optode.Detector};
+Optode.Source = struct();
+Optode.Source = copycfg(cfg, 'srcpos', Optode.Source, 'Pos');
+Optode.Source = copycfg(cfg, 'srcdir', Optode.Source, 'Dir');
+Optode.Source = copycfg(cfg, 'srcparam1', Optode.Source, 'Param1');
+Optode.Source = copycfg(cfg, 'srcparam2', Optode.Source, 'Param2');
+Optode.Source = copycfg(cfg, 'srctype', Optode.Source, 'Type');
+Optode.Source = copycfg(cfg, 'srcnum', Optode.Source, 'SrcNum');
+
+if (isfield(cfg, 'detpos') && ~isempty(cfg.detpos))
+    Optode.Detector = struct();
+    Optode.Detector = cell2struct(mat2cell(cfg.detpos, ones(1, size(cfg.detpos, 1)), [3 1]), {'Pos', 'R'}, 2);
+    if (length(Optode.Detector) == 1)
+        Optode.Detector = {Optode.Detector};
     end
 end
-if(isfield(cfg,'srcpattern') && ~isempty(cfg.srcpattern))
-    Optode.Source.Pattern.Nx=size(cfg.srcpattern,1);
-    Optode.Source.Pattern.Ny=size(cfg.srcpattern,2);
-    Optode.Source.Pattern.Nz=size(cfg.srcpattern,3);
-    Optode.Source.Pattern.Data=single(cfg.srcpattern);
-    if(~singlefile)
-        Optode.Source.Pattern.Data=[filestub '_pattern.bin'];
-        fid=fopen(Optode.Source.Pattern.Data,'wb');
-        fwrite(fid,cfg.srcpattern,'float32');
+if (isfield(cfg, 'srcpattern') && ~isempty(cfg.srcpattern))
+    Optode.Source.Pattern.Nx = size(cfg.srcpattern, 1);
+    Optode.Source.Pattern.Ny = size(cfg.srcpattern, 2);
+    Optode.Source.Pattern.Nz = size(cfg.srcpattern, 3);
+    Optode.Source.Pattern.Data = single(cfg.srcpattern);
+    if (~singlefile)
+        Optode.Source.Pattern.Data = [filestub '_pattern.bin'];
+        fid = fopen(Optode.Source.Pattern.Data, 'wb');
+        fwrite(fid, cfg.srcpattern, 'float32');
         fclose(fid);
     end
 end
 
 %% define the domain and optical properties
 
-Mesh=struct();
-Mesh=copycfg(cfg,'unitinmm',Mesh,'LengthUnit');
+Mesh = struct();
+Mesh = copycfg(cfg, 'unitinmm', Mesh, 'LengthUnit');
 
-if(isfield(cfg,'node') && ~isempty(cfg.node) && isfield(cfg,'elem') && ~isempty(cfg.elem))
-    node=cfg.node;
-    elem=cfg.elem;
-    if(isfield(cfg,'elemprop') && size(elem,2)==4)
-        elem=[elem, cfg.elemprop];
+if (isfield(cfg, 'node') && ~isempty(cfg.node) && isfield(cfg, 'elem') && ~isempty(cfg.elem))
+    node = cfg.node;
+    elem = cfg.elem;
+    if (isfield(cfg, 'elemprop') && size(elem, 2) == 4)
+        elem = [elem, cfg.elemprop];
     end
-    if(~singlefile)
-        savemmcmesh(fname,node,elem);
+    if (~singlefile)
+        savemmcmesh(fname, node, elem);
     else
-        Mesh.MeshNode=single(node);
-        Mesh.MeshElem=uint32(elem);
-        if(isfield(cfg, 'edgeroi'))
-            Mesh.MeshROI=single(cfg.edgeroi);
-        elseif(isfield(cfg,'noderoi'))
-            Mesh.MeshROI=single(cfg.noderoi);
-        elseif(isfield(cfg,'faceroi'))
-            Mesh.MeshROI=single(cfg.faceroi);
+        Mesh.MeshNode = single(node);
+        Mesh.MeshElem = uint32(elem);
+        if (isfield(cfg, 'edgeroi'))
+            Mesh.MeshROI = single(cfg.edgeroi);
+        elseif (isfield(cfg, 'noderoi'))
+            Mesh.MeshROI = single(cfg.noderoi);
+        elseif (isfield(cfg, 'faceroi'))
+            Mesh.MeshROI = single(cfg.faceroi);
         end
     end
 
-    if(~isfield(cfg,'e0'))
-        cfg.e0=tsearchn(node,elem(:,1:4),cfg.srcpos);
+    if (~isfield(cfg, 'e0'))
+        cfg.e0 = tsearchn(node, elem(:, 1:4), cfg.srcpos);
     end
-    Mesh=copycfg(cfg,'e0',Mesh,'InitElem');
+    Mesh = copycfg(cfg, 'e0', Mesh, 'InitElem');
 
 else
-    Mesh.MeshID=fname;
-    warning('mesh is missing!')
+    Mesh.MeshID = fname;
+    warning('mesh is missing!');
 end
 
-Domain=struct();
-Domain=copycfg(cfg,'steps',Domain,'Step');
-if(isfield(cfg,'prop'))
-    prop=[(1:size(cfg.prop,1)-1)' cfg.prop(2:end,:)];
-    if(~singlefile)
-        fid=fopen(['prop_',fname,'.dat'],'wt');
-        fprintf(fid,'1 %d\n',size(prop,1));
-        fprintf(fid,'%d %e %e %e %e\n',prop');
+Domain = struct();
+Domain = copycfg(cfg, 'steps', Domain, 'Step');
+if (isfield(cfg, 'prop'))
+    prop = [(1:size(cfg.prop, 1) - 1)' cfg.prop(2:end, :)];
+    if (~singlefile)
+        fid = fopen(['prop_', fname, '.dat'], 'wt');
+        fprintf(fid, '1 %d\n', size(prop, 1));
+        fprintf(fid, '%d %e %e %e %e\n', prop');
         fclose(fid);
     else
         Domain.Media = cell2struct(num2cell(cfg.prop), {'mua', 'mus', 'g', 'n'}, 2)';
@@ -117,74 +117,73 @@
 
 %% define the simulation session flags
 
-Session=struct();
-if(exist('fname', 'var'))
-    Session.ID=fname;
+Session = struct();
+if (exist('fname', 'var'))
+    Session.ID = fname;
 else
-    Session.ID=inputname(1);
+    Session.ID = inputname(1);
 end
-Session=copycfg(cfg,'isreflect',Session,'DoMismatch');
-Session=copycfg(cfg,'issave2pt',Session,'DoSaveVolume');
-Session=copycfg(cfg,'issavedet',Session,'DoPartialPath');
-Session=copycfg(cfg,'issaveexit',Session,'DoSaveExit');
-Session=copycfg(cfg,'issaveseed',Session,'DoSaveSeed');
-Session=copycfg(cfg,'isnormalize',Session,'DoNormalize');
-Session=copycfg(cfg,'ismomentum',Session,'DoDCS');
-Session=copycfg(cfg,'isspecular',Session,'DoSpecular');
-Session=copycfg(cfg,'outputformat',Session,'OutputFormat');
-Session=copycfg(cfg,'debuglevel',Session,'DebugFlag');
-Session=copycfg(cfg,'autopilot',Session,'DoAutoThread');
-Session=copycfg(cfg,'basisorder',Session,'BasisOrder');
-
-if(isfield(cfg,'method'))
-    methodmap=struct('plucker', 'p', 'havel', 'h', 'badouel', 'b', 'elem', 's', 'grid', 'g');
-    if(isfield(methodmap, cfg.method))
-        Session.RayTracer=methodmap.(cfg.method);
+Session = copycfg(cfg, 'isreflect', Session, 'DoMismatch');
+Session = copycfg(cfg, 'issave2pt', Session, 'DoSaveVolume');
+Session = copycfg(cfg, 'issavedet', Session, 'DoPartialPath');
+Session = copycfg(cfg, 'issaveexit', Session, 'DoSaveExit');
+Session = copycfg(cfg, 'issaveseed', Session, 'DoSaveSeed');
+Session = copycfg(cfg, 'isnormalize', Session, 'DoNormalize');
+Session = copycfg(cfg, 'ismomentum', Session, 'DoDCS');
+Session = copycfg(cfg, 'isspecular', Session, 'DoSpecular');
+Session = copycfg(cfg, 'outputformat', Session, 'OutputFormat');
+Session = copycfg(cfg, 'debuglevel', Session, 'DebugFlag');
+Session = copycfg(cfg, 'autopilot', Session, 'DoAutoThread');
+Session = copycfg(cfg, 'basisorder', Session, 'BasisOrder');
+
+if (isfield(cfg, 'method'))
+    methodmap = struct('plucker', 'p', 'havel', 'h', 'badouel', 'b', 'elem', 's', 'grid', 'g');
+    if (isfield(methodmap, cfg.method))
+        Session.RayTracer = methodmap.(cfg.method);
     else
-        error('cfg.method is invalid')
+        error('cfg.method is invalid');
     end
 end
 
-if(isfield(cfg,'outputtype'))
-    outputtypemap=struct('flux', 'x', 'fluence', 'f', 'energy', 'e', 'jacobian', 'j', 'wl', 'l', 'wp', 'p');
-    if(isfield(outputtypemap, cfg.outputtype))
-        Session.OutputType=outputtypemap.(cfg.outputtype);
+if (isfield(cfg, 'outputtype'))
+    outputtypemap = struct('flux', 'x', 'fluence', 'f', 'energy', 'e', 'jacobian', 'j', 'wl', 'l', 'wp', 'p');
+    if (isfield(outputtypemap, cfg.outputtype))
+        Session.OutputType = outputtypemap.(cfg.outputtype);
     else
-        error('cfg.outputtype is invalid')
+        error('cfg.outputtype is invalid');
     end
 end
 
-if(isfield(cfg,'seed') && numel(cfg.seed)==1)
-    Session.RNGSeed=cfg.seed;
+if (isfield(cfg, 'seed') && numel(cfg.seed) == 1)
+    Session.RNGSeed = cfg.seed;
 end
-Session=copycfg(cfg,'nphoton',Session,'Photons');
-%Session=copycfg(cfg,'rootpath',Session,'RootPath');
+Session = copycfg(cfg, 'nphoton', Session, 'Photons');
+% Session=copycfg(cfg,'rootpath',Session,'RootPath');
 
 %% define the forward simulation settings
 
-Forward.T0=cfg.tstart;
-Forward.T1=cfg.tend;
-Forward.Dt=cfg.tstep;
-Forward=copycfg(cfg,'nout',Forward,'N0');
+Forward.T0 = cfg.tstart;
+Forward.T1 = cfg.tend;
+Forward.Dt = cfg.tstep;
+Forward = copycfg(cfg, 'nout', Forward, 'N0');
 
 %% assemble the complete input, save to a JSON or UBJSON input file
 
-mmcsession=struct('Session', Session, 'Domain', Domain, 'Mesh', Mesh, 'Forward', Forward, 'Optode',Optode);
+mmcsession = struct('Session', Session, 'Domain', Domain, 'Mesh', Mesh, 'Forward', Forward, 'Optode', Optode);
 
-if(nargin == 1)
-    [varargout{1:nargout}] = savejson('',mmcsession, varargin{:});
-elseif(strcmp(fext,'ubj'))
-    [varargout{1:nargout}] = saveubjson('',mmcsession,'filename',[filestub,'.ubj'], varargin{:});
+if (nargin == 1)
+    [varargout{1:nargout}] = savejson('', mmcsession, varargin{:});
+elseif (strcmp(fext, 'ubj'))
+    [varargout{1:nargout}] = saveubjson('', mmcsession, 'filename', [filestub, '.ubj'], varargin{:});
 else
-    [varargout{1:nargout}] = savejson('',mmcsession,'filename', [filestub,'.json'], varargin{:});
+    [varargout{1:nargout}] = savejson('', mmcsession, 'filename', [filestub, '.json'], varargin{:});
 end
 
-
-function outdata=copycfg(cfg,name,outroot,outfield,defaultval)
-if(nargin>=5)
-    outroot.(outfield)=defaultval;
+function outdata = copycfg(cfg, name, outroot, outfield, defaultval)
+if (nargin >= 5)
+    outroot.(outfield) = defaultval;
 end
-if(isfield(cfg,name))
-    outroot.(outfield)=cfg.(name);
+if (isfield(cfg, name))
+    outroot.(outfield) = cfg.(name);
 end
-outdata=outroot;
+outdata = outroot;
diff --git a/mmclab/mmclab.m b/mmclab/mmclab.m
index 08b1fb9d..98f0dba6 100644
--- a/mmclab/mmclab.m
+++ b/mmclab/mmclab.m
@@ -1,23 +1,23 @@
-function varargout=mmclab(varargin)
+function varargout = mmclab(varargin)
 %
-%#############################################################################%
+% #############################################################################%
 %                     Mesh-based Monte Carlo (MMC) - OpenCL                   %
 %          Copyright (c) 2010-2024 Qianqian Fang <q.fang at neu.edu>          %
 %              https://mcx.space/#mmc  &  https://neurojson.io/               %
 %                                                                             %
-%Computational Optics & Translational Imaging (COTI) Lab  [http://fanglab.org]%
+% Computational Optics & Translational Imaging (COTI) Lab  [http://fanglab.org]%
 %   Department of Bioengineering, Northeastern University, Boston, MA, USA    %
-%#############################################################################%
+% #############################################################################%
 %    The MCX Project is funded by the NIH/NIGMS under grant R01-GM114365      %
-%#############################################################################%
+% #############################################################################%
 %  Open-source codes and reusable scientific data are essential for research, %
 % MCX proudly developed human-readable JSON-based data formats for easy reuse.%
 %                                                                             %
-%Please visit our free scientific data sharing portal at https://neurojson.io/%
+% Please visit our free scientific data sharing portal at https://neurojson.io/%
 % and consider sharing your public datasets in standardized JSON/JData format %
-%#############################################################################%
-%$Rev::      $v2024.2$Date::                       $ by $Author::Qianqian Fang%
-%#############################################################################%
+% #############################################################################%
+% $Rev::      $v2024.2$Date::                       $ by $Author::Qianqian Fang%
+% #############################################################################%
 %
 % Format:
 %    [fluence,detphoton,ncfg,seeds,traj]=mmclab(cfg);
@@ -27,8 +27,8 @@
 %    [fluence,detphoton,ncfg,seeds,traj]=mmclab(cfg, options);
 %
 % Input:
-%    cfg: a struct, or struct array. Each element in cfg defines 
-%         a set of parameters for a simulation. 
+%    cfg: a struct, or struct array. Each element in cfg defines
+%         a set of parameters for a simulation.
 %
 %    option: (optional), options is a string, specifying additional options
 %         option='preview': this plots the domain configuration using mcxpreview(cfg)
@@ -38,10 +38,10 @@
 %
 %    cfg may contain the following fields:
 %
-%== Required ==
+% == Required ==
 %     *cfg.nphoton:     the total number of photons to be simulated (integer)
 %     *cfg.prop:        an N by 4 array, each row specifies [mua, mus, g, n] in order.
-%                       the first row corresponds to medium type 0 which is 
+%                       the first row corresponds to medium type 0 which is
 %                       typically [0 0 1 1]. The second row is type 1, and so on.
 %     *cfg.node:        node array for the input tetrahedral mesh, 3 columns: (x,y,z)
 %     *cfg.elem:        element array for the input tetrahedral mesh, 4 columns
@@ -52,17 +52,17 @@
 %     *cfg.srcpos:      a 1 by 3 vector, the position of the source in mesh node length unit
 %     *cfg.srcdir:      if defined as [vx, vy, vy], it specifies the incident vector
 %                       if defined as [vx, vy, vy, focus], the first 3 elements define
-%                       the incident vector; focus controls the convergence or 
+%                       the incident vector; focus controls the convergence or
 %                       divergence of the beam:
 %                       focus=0: collimated beam
 %                       focus<0: diverging beam from an imaginary src at c0-|focus|*[vx vy vz]
 %                       focus>0: converging beam, focusing to a point at c0+|focus|*[vx vy vz]
-%                       where c0 is the centroid of the source domain. Setting focus does 
+%                       where c0 is the centroid of the source domain. Setting focus does
 %                       not impact pencil/isotropic/cone sources.
 %
-%== MC simulation settings ==
+% == MC simulation settings ==
 %      cfg.seed:        seed for the random number generator (integer)
-%                       if set to a uint8 array, the binary data in each column is used 
+%                       if set to a uint8 array, the binary data in each column is used
 %                       to seed a photon (i.e. the "replay" mode), default value: 1648335518
 %      cfg.isreflect:   [1]-consider refractive index mismatch, 0-matched index
 %                       2 - total absorption on exterior surface
@@ -71,7 +71,7 @@
 %      cfg.isspecular:  [1]-calculate specular reflection if source is outside
 %      cfg.ismomentum:  [0]-save momentum transfer for each detected photon
 %      cfg.method:      ray-tracing method, ["plucker"]:Plucker, "havel": Havel (SSE4),
-%                       "badouel": partial Badouel, "elem": branchless Badouel (SSE), 
+%                       "badouel": partial Badouel, "elem": branchless Badouel (SSE),
 %                       "grid": dual-grid MMC
 %      cfg.mcmethod:    0 use MCX-styled MC method, 1 use MCML style MC
 %      cfg.nout:        [1.0] refractive index for medium type 0 (background)
@@ -80,33 +80,33 @@
 %      cfg.steps:       [dx, dy, dz], defines the DMMC grid voxel size,
 %                       must be isostropic, i.e. dx=dy=dz, only used when
 %                       cfg.method = 'grid', by default dx=dy=dz=1
-%      cfg.unitinmm:    defines the default length unit (to interpret mesh nodes, src/det positions 
-%                       the default value is 1.0 (mm). For example, if the mesh node length unit is 
+%      cfg.unitinmm:    defines the default length unit (to interpret mesh nodes, src/det positions
+%                       the default value is 1.0 (mm). For example, if the mesh node length unit is
 %                       in cm, one should set unitinmm to 10.
 %      cfg.basisorder:  [1]-linear basis, 0-piece-wise constant basis
 %
-%== Source-detector parameters ==
+% == Source-detector parameters ==
 %      cfg.detpos:      an N by 4 array, each row specifying a detector: [x,y,z,radius]
 %      cfg.maxdetphoton:   maximum number of photons saved by the detectors [1000000]
 %      cfg.srctype:     source type, the parameters of the src are specified by cfg.srcparam{1,2}
 %                      'pencil' - default, pencil beam, no param needed
 %                      'isotropic' - isotropic source, no param needed
 %                      'cone' - uniform cone beam, srcparam1(1) is the half-angle in radian
-%                      'gaussian' - a gaussian beam, srcparam1(1) specifies the waist radius 
+%                      'gaussian' - a gaussian beam, srcparam1(1) specifies the waist radius
 %                                (in default length unit); if one specifies a non-zero focal length
-%                                using cfg.srcdir, the gaussian beam can be converging to or 
+%                                using cfg.srcdir, the gaussian beam can be converging to or
 %                                diverging from the waist center, which is located at srcpos+focus*srcdir;
-%                                optionally, one can specify the wavelength lambda (in cfg.unitinmm mm), 
-%                                using srcparam1(2). This will rescale the Gaussian profile according 
-%                                to w(z)=w0*sqrt(1-(z/z0)^2), where w0 is the waist radius, z is the 
-%                                distance (in mm) to the waist center (focus), and z0 is the Rayleigh 
+%                                optionally, one can specify the wavelength lambda (in cfg.unitinmm mm),
+%                                using srcparam1(2). This will rescale the Gaussian profile according
+%                                to w(z)=w0*sqrt(1-(z/z0)^2), where w0 is the waist radius, z is the
+%                                distance (in mm) to the waist center (focus), and z0 is the Rayleigh
 %                                range (in mm), and z0 is related to w0 by z0=w0^2*pi/lambda
-%                      'planar' - a 3D quadrilateral uniform planar source, with three corners specified 
+%                      'planar' - a 3D quadrilateral uniform planar source, with three corners specified
 %                                by srcpos, srcpos+srcparam1(1:3) and srcpos+srcparam2(1:3)
 %                      'pattern' - a 3D quadrilateral pattern illumination, same as above, except
 %                                srcparam1(4) and srcparam2(4) specify the pattern array x/y dimensions,
-%                                and srcpattern is a floating-point pattern array, with values between [0-1]. 
-%                                if cfg.srcnum>1, srcpattern must be a floating-point array with 
+%                                and srcpattern is a floating-point pattern array, with values between [0-1].
+%                                if cfg.srcnum>1, srcpattern must be a floating-point array with
 %                                a dimension of [srcnum srcparam1(4) srcparam2(4)]
 %                                Example: <demo_photon_sharing.m>
 %                      'fourier' - spatial frequency domain source, similar to 'planar', except
@@ -117,16 +117,16 @@
 %                                    S=0.5*[1+M*cos(2*pi*(fx*x+fy*y)+phi0)], (0<=x,y,M<=1)
 %                      'arcsine' - similar to isotropic, except the zenith angle is uniform
 %                                distribution, rather than a sine distribution.
-%                      'disk' - a uniform disk source pointing along srcdir; the radius is 
+%                      'disk' - a uniform disk source pointing along srcdir; the radius is
 %                               set by srcparam1(1) (in default length unit)
-%                      'fourierx' - a general Fourier source, the parameters are 
+%                      'fourierx' - a general Fourier source, the parameters are
 %                               srcparam1: [v1x,v1y,v1z,|v2|], srcparam2: [kx,ky,phi0,M]
 %                               normalized vectors satisfy: srcdir cross v1=v2
 %                               the phase shift is phi0*2*pi
 %                      'fourierx2d' - a general 2D Fourier basis, parameters
 %                               srcparam1: [v1x,v1y,v1z,|v2|], srcparam2: [kx,ky,phix,phiy]
 %                               the phase shift is phi{x,y}*2*pi
-%                      'zgaussian' - an angular gaussian beam, srcparam1(1) specifies the variance in  
+%                      'zgaussian' - an angular gaussian beam, srcparam1(1) specifies the variance in
 %                               the zenith angle
 %      cfg.{srcparam1,srcparam2}: 1x4 vectors, see cfg.srctype for details
 %      cfg.srcpattern: see cfg.srctype for details
@@ -144,7 +144,7 @@
 %      if the mesh coordinates/source positions are not in mm unit, one needs to define
 %      cfg.unitinmm  (in mm) to specify the actual length unit.
 %
-%== Optional mesh data ==
+% == Optional mesh data ==
 %     -cfg.facenb:      element face neighbohood list (calculated by faceneighbors())
 %     -cfg.evol:        element volume (calculated by elemvolume() with iso2mesh)
 %     -cfg.e0:          the element ID enclosing the source, if not defined,
@@ -156,7 +156,7 @@
 %                       '<': search along the backward direction
 %                       '-': search both directions
 %
-%== Output control ==
+% == Output control ==
 %      cfg.issaveexit: [0]-save the position (x,y,z) and (vx,vy,vz) for a detected photon
 %      cfg.issaveref:  [0]-save diffuse reflectance/transmittance on the exterior surfaces.
 %                      The output is stored as flux.dref in a 2D array of size [#Nf,  #time_gate]
@@ -168,8 +168,8 @@
 %      cfg.issaveseed:  [0]-save the RNG seed for a detected photon so one can replay
 %      cfg.isatomic:    [1]-use atomic operations for saving fluence, 0-no atomic operations
 %      cfg.outputtype:  'flux' - output fluence-rate
-%                       'fluence' - fluence, 
-%                       'energy' - energy deposit, 
+%                       'fluence' - fluence,
+%                       'energy' - energy deposit,
 %                       'jacobian' - mua Jacobian (replay mode)
 %                       'wl'- weighted path lengths to build mua Jacobian (replay mode)
 %                       'wp'- weighted scattering counts to build mus Jacobian (replay mode)
@@ -184,15 +184,15 @@
 %
 %
 %    type: omit or 'omp' for multi-threading version; 'sse' for the SSE4 MMC,
-%          the SSE4 version is about 25% faster, but requires newer CPUs; 
+%          the SSE4 version is about 25% faster, but requires newer CPUs;
 %          if type='prep' with a single output, mmclab returns ncfg only.
 %
 % Output:
 %      fluence: a struct array, with a length equals to that of cfg.
 %            For each element of fluence, fluence(i).data is a 2D array with
 %            dimensions [size(cfg.node,1), total-time-gates] if cfg.basisorder=1,
-%            or [size(cfg.elem,1), total-time-gates] if cfg.basisorder=0. 
-%            The content of the array is the normalized fluence-rate (or others 
+%            or [size(cfg.elem,1), total-time-gates] if cfg.basisorder=0.
+%            The content of the array is the normalized fluence-rate (or others
 %            depending on cfg.outputtype) at each mesh node and time-gate.
 %
 %            If cfg.issaveref is set to 1, fluence(i).dref is not empty, and stores
@@ -255,225 +255,224 @@
 %
 
 try
-    defaultocl=evalin('base','USE_MCXCL');
+    defaultocl = evalin('base', 'USE_MCXCL');
 catch
-    defaultocl=1;
+    defaultocl = 1;
 end
 
-useopencl=defaultocl;
+useopencl = defaultocl;
 
-if(nargin==2 && ischar(varargin{2}))
-    if(strcmp(varargin{2},'preview') || strcmp(varargin{2},'prep') || strcmp(varargin{2},'cuda'))
-        useopencl=0;
+if (nargin == 2 && ischar(varargin{2}))
+    if (strcmp(varargin{2}, 'preview') || strcmp(varargin{2}, 'prep') || strcmp(varargin{2}, 'cuda'))
+        useopencl = 0;
     end
 end
 
-if(isstruct(varargin{1}))
-    for i=1:length(varargin{1})
-        castlist={'srcpattern','srcpos','detpos','prop','workload','srcdir'};
-        for j=1:length(castlist)
-            if(isfield(varargin{1}(i),castlist{j}))
-                varargin{1}(i).(castlist{j})=double(varargin{1}(i).(castlist{j}));
+if (isstruct(varargin{1}))
+    for i = 1:length(varargin{1})
+        castlist = {'srcpattern', 'srcpos', 'detpos', 'prop', 'workload', 'srcdir'};
+        for j = 1:length(castlist)
+            if (isfield(varargin{1}(i), castlist{j}))
+                varargin{1}(i).(castlist{j}) = double(varargin{1}(i).(castlist{j}));
             end
         end
     end
 end
 
-if(nargin==1 && ischar(varargin{1}) && strcmp(varargin{1},'gpuinfo'))
-    varargout{1}=mmc('gpuinfo');
-    return;
+if (nargin == 1 && ischar(varargin{1}) && strcmp(varargin{1}, 'gpuinfo'))
+    varargout{1} = mmc('gpuinfo');
+    return
 end
 
-if(nargin==0)
-    return;
+if (nargin == 0)
+    return
 end
 
-cfg=varargin{1};
-if(length(varargin)>=2)
-    type=varargin{2};
+cfg = varargin{1};
+if (length(varargin) >= 2)
+    type = varargin{2};
 end
-    
-if(~isstruct(cfg))
+
+if (~isstruct(cfg))
     error('cfg must be a struct or struct array');
 end
 
-len=length(cfg);
-for i=1:len
-    if(~isfield(cfg(i),'node') || ~isfield(cfg(i),'elem'))
+len = length(cfg);
+for i = 1:len
+    if (~isfield(cfg(i), 'node') || ~isfield(cfg(i), 'elem'))
         error('cfg.node or cfg.elem is missing');
     end
-    if(size(cfg(i).elem,2)>4)
-        cfg(i).elemprop=cfg(i).elem(:,5);
+    if (size(cfg(i).elem, 2) > 4)
+        cfg(i).elemprop = cfg(i).elem(:, 5);
     end
-    if(~isfield(cfg(i),'isreoriented') || isempty(cfg(i).isreoriented) || cfg(i).isreoriented==0)
-        if(isfield(cfg(i),'edgeroi') || isfield(cfg(i),'faceroi'))
-            [cfg(i).elem, evol, idx]=meshreorient(cfg(i).node,cfg(i).elem(:,1:4));
-	else
-	    [cfg(i).elem, evol]=meshreorient(cfg(i).node,cfg(i).elem(:,1:4));
-	end
-	if(isfield(cfg(i),'edgeroi'))
-	    cfg(i).edgeroi(idx,:)=cfg(i).edgeroi(idx,[1 3 2 5 4 6]);
-	end
-	if(isfield(cfg(i),'faceroi'))
-	    cfg(i).faceroi(idx,:)=cfg(i).faceroi(idx,[2 1 3 4]);
-	end
-        cfg(i).isreoriented=1;
+    if (~isfield(cfg(i), 'isreoriented') || isempty(cfg(i).isreoriented) || cfg(i).isreoriented == 0)
+        if (isfield(cfg(i), 'edgeroi') || isfield(cfg(i), 'faceroi'))
+            [cfg(i).elem, evol, idx] = meshreorient(cfg(i).node, cfg(i).elem(:, 1:4));
+        else
+            [cfg(i).elem, evol] = meshreorient(cfg(i).node, cfg(i).elem(:, 1:4));
+        end
+        if (isfield(cfg(i), 'edgeroi'))
+            cfg(i).edgeroi(idx, :) = cfg(i).edgeroi(idx, [1 3 2 5 4 6]);
+        end
+        if (isfield(cfg(i), 'faceroi'))
+            cfg(i).faceroi(idx, :) = cfg(i).faceroi(idx, [2 1 3 4]);
+        end
+        cfg(i).isreoriented = 1;
     end
-    if(~isfield(cfg(i),'facenb') || isempty(cfg(i).facenb))
-        cfg(i).facenb=faceneighbors(cfg(i).elem);
+    if (~isfield(cfg(i), 'facenb') || isempty(cfg(i).facenb))
+        cfg(i).facenb = faceneighbors(cfg(i).elem);
     end
-    if(~isfield(cfg(i),'evol') || isempty(cfg(i).evol))
-        cfg(i).evol=elemvolume(cfg(i).node,cfg(i).elem);
+    if (~isfield(cfg(i), 'evol') || isempty(cfg(i).evol))
+        cfg(i).evol = elemvolume(cfg(i).node, cfg(i).elem);
     end
-    if(find(cfg(i).evol==0))
-        fprintf(1,['degenerated elements are detected: [' sprintf('%d ',find(cfg(i).evol==0)) ']\n']);
+    if (find(cfg(i).evol == 0))
+        fprintf(1, ['degenerated elements are detected: [' sprintf('%d ', find(cfg(i).evol == 0)) ']\n']);
         error(['input mesh can not contain degenerated elements, ' ...
-            'please double check your input mesh; if you use a ' ...
-            'widefield source, please rerun mmcsrcdomain and setting ' ...
-            '''Expansion'' option to a larger value (default is 1)']);
+               'please double check your input mesh; if you use a ' ...
+               'widefield source, please rerun mmcsrcdomain and setting ' ...
+               '''Expansion'' option to a larger value (default is 1)']);
     end
-    if(~isfield(cfg(i),'srcpos'))
+    if (~isfield(cfg(i), 'srcpos'))
         error('cfg.srcpos field is missing');
     end
-    if(~isfield(cfg(i),'srcdir'))
+    if (~isfield(cfg(i), 'srcdir'))
         error('cfg.srcdir field is missing');
     end
-    if(~isfield(cfg(i),'e0') || isempty(cfg(i).e0))
-        cfg(i).e0=tsearchn(cfg(i).node,cfg(i).elem,cfg(i).srcpos);
+    if (~isfield(cfg(i), 'e0') || isempty(cfg(i).e0))
+        cfg(i).e0 = tsearchn(cfg(i).node, cfg(i).elem, cfg(i).srcpos);
     end
-    if((isnan(cfg(i).e0) && (isfield(cfg(i),'srctype') ...
-            && strcmp(cfg(i).srctype,'pencil')) )|| ischar(cfg(i).e0))
+    if ((isnan(cfg(i).e0) && (isfield(cfg(i), 'srctype') && strcmp(cfg(i).srctype, 'pencil'))) || ischar(cfg(i).e0))
         disp('searching initial element ...');
-        [cfg(i).srcpos,cfg(i).e0]=mmcraytrace(cfg(i).node,cfg(i).elem,cfg(i).srcpos,cfg(i).srcdir,cfg(i).e0);
+        [cfg(i).srcpos, cfg(i).e0] = mmcraytrace(cfg(i).node, cfg(i).elem, cfg(i).srcpos, cfg(i).srcdir, cfg(i).e0);
     end
-    if((isfield(cfg(i),'srctype') && strcmp(cfg(i).srctype,'pattern')) && (ndims(cfg(i).srcpattern)==2))
-        cfg(i).srcpattern=reshape(cfg(i).srcpattern,...
-            size(cfg(i).srcpattern,1),size(cfg(i).srcpattern,2),1);
+    if ((isfield(cfg(i), 'srctype') && strcmp(cfg(i).srctype, 'pattern')) && (ndims(cfg(i).srcpattern) == 2))
+        cfg(i).srcpattern = reshape(cfg(i).srcpattern, ...
+                                    size(cfg(i).srcpattern, 1), size(cfg(i).srcpattern, 2), 1);
     end
-    if(isnan(cfg(i).e0))  % widefield source
-        if(~isfield(cfg(i),'srcparam1') || ~isfield(cfg(i),'srcparam2'))
+    if (isnan(cfg(i).e0))  % widefield source
+        if (~isfield(cfg(i), 'srcparam1') || ~isfield(cfg(i), 'srcparam2'))
             error('for wide-field sources, you must provide srcparam1 and srcparam2');
         end
-        if(~isfield(cfg(i),'srctype'))
-            cfg(i).srctype='pencil';
+        if (~isfield(cfg(i), 'srctype'))
+            cfg(i).srctype = 'pencil';
         end
-        srcdef=struct('srctype',cfg.srctype,'srcpos',cfg.srcpos,'srcdir',cfg.srcdir,...
-            'srcparam1',cfg.srcparam1,'srcparam2',cfg.srcparam2);
-        sdom=mmcsrcdomain(srcdef,[min(cfg.node);max(cfg.node)]);
-        isinside=ismember(round(sdom*1e10)*1e-10,round(cfg(i).node*1e10)*1e-10,'rows');
-        if(all(~isinside))
-            if(size(cfg(i).elem,2)==4)
-                cfg(i).elem(:,5)=1;
+        srcdef = struct('srctype', cfg.srctype, 'srcpos', cfg.srcpos, 'srcdir', cfg.srcdir, ...
+                        'srcparam1', cfg.srcparam1, 'srcparam2', cfg.srcparam2);
+        sdom = mmcsrcdomain(srcdef, [min(cfg.node); max(cfg.node)]);
+        isinside = ismember(round(sdom * 1e10) * 1e-10, round(cfg(i).node * 1e10) * 1e-10, 'rows');
+        if (all(~isinside))
+            if (size(cfg(i).elem, 2) == 4)
+                cfg(i).elem(:, 5) = 1;
             end
-            [cfg(i).node,cfg(i).elem] = mmcaddsrc(cfg(i).node,cfg(i).elem,sdom);
-            cfg(i).elemprop=cfg(i).elem(:,5);
-            if(isfield(cfg(i),'edgeroi') || isfield(cfg(i),'faceroi'))
-                [cfg(i).elem, evol, idx]=meshreorient(cfg(i).node,cfg(i).elem(:,1:4));
+            [cfg(i).node, cfg(i).elem] = mmcaddsrc(cfg(i).node, cfg(i).elem, sdom);
+            cfg(i).elemprop = cfg(i).elem(:, 5);
+            if (isfield(cfg(i), 'edgeroi') || isfield(cfg(i), 'faceroi'))
+                [cfg(i).elem, evol, idx] = meshreorient(cfg(i).node, cfg(i).elem(:, 1:4));
             else
-                [cfg(i).elem, evol]=meshreorient(cfg(i).node,cfg(i).elem(:,1:4));
+                [cfg(i).elem, evol] = meshreorient(cfg(i).node, cfg(i).elem(:, 1:4));
             end
-            if(isfield(cfg(i),'edgeroi'))
-	        cfg(i).edgeroi(idx,:)=cfg(i).edgeroi(idx,[1 3 2 5 4 6]);
+            if (isfield(cfg(i), 'edgeroi'))
+                cfg(i).edgeroi(idx, :) = cfg(i).edgeroi(idx, [1 3 2 5 4 6]);
             end
-            if(isfield(cfg(i),'faceroi'))
-	        cfg(i).faceroi(idx,:)=cfg(i).faceroi(idx,[2 1 3 4]);
+            if (isfield(cfg(i), 'faceroi'))
+                cfg(i).faceroi(idx, :) = cfg(i).faceroi(idx, [2 1 3 4]);
             end
-            cfg(i).facenb=faceneighbors(cfg(i).elem);
-            cfg(i).evol=elemvolume(cfg(i).node,cfg(i).elem);
-            cfg(i).isreoriented=1;
+            cfg(i).facenb = faceneighbors(cfg(i).elem);
+            cfg(i).evol = elemvolume(cfg(i).node, cfg(i).elem);
+            cfg(i).isreoriented = 1;
         end
-        if(strcmp(cfg(i).srctype,'pencil') || strcmp(cfg(i).srctype,'isotropic') ...
-                || strcmp(cfg(i).srctype,'cone')   || strcmp(cfg(i).srctype,'zgaussian'))
-            cfg(i).e0=tsearchn(cfg(i).node,cfg(i).elem,cfg(i).srcpos);
-            if(isnan(cfg(i).e0))
-                cfg(i).e0=-1;
+        if (strcmp(cfg(i).srctype, 'pencil') || strcmp(cfg(i).srctype, 'isotropic') || ...
+            strcmp(cfg(i).srctype, 'cone')   || strcmp(cfg(i).srctype, 'zgaussian'))
+            cfg(i).e0 = tsearchn(cfg(i).node, cfg(i).elem, cfg(i).srcpos);
+            if (isnan(cfg(i).e0))
+                cfg(i).e0 = -1;
             end
-        elseif(length(find(cfg(i).elemprop<0))==1)
-            cfg(i).e0=find(cfg(i).elemprop<0);
+        elseif (length(find(cfg(i).elemprop < 0)) == 1)
+            cfg(i).e0 = find(cfg(i).elemprop < 0);
         else
-            cfg(i).e0=-1;
+            cfg(i).e0 = -1;
         end
     end
-    if(~isfield(cfg(i),'elemprop'))
+    if (~isfield(cfg(i), 'elemprop'))
         error('cfg.elemprop field is missing');
     end
-    if(~isfield(cfg(i),'nphoton'))
+    if (~isfield(cfg(i), 'nphoton'))
         error('cfg.nphoton field is missing');
     end
-    if(~isfield(cfg(i),'prop') || size(cfg(i).prop,1)<max(cfg(i).elemprop)+1 || min(cfg(i).elemprop<=0))
+    if (~isfield(cfg(i), 'prop') || size(cfg(i).prop, 1) < max(cfg(i).elemprop) + 1 || min(cfg(i).elemprop <= 0))
         error('cfg.prop field is missing or insufficient');
     end
 end
 
 % must do a fflush, otherwise octave buffers the output until complete
-if(exist('OCTAVE_VERSION'))
+if (exist('OCTAVE_VERSION'))
     fflush(stdout);
 end
 
-if(exist('maxNumCompThreads','file'))
-    warning('off','MATLAB:maxNumCompThreads:Deprecated');
+if (exist('maxNumCompThreads', 'file'))
+    warning('off', 'MATLAB:maxNumCompThreads:Deprecated');
     maxNumCompThreads('automatic');
-    maxNumCompThreads(maxNumCompThreads*2);
+    maxNumCompThreads(maxNumCompThreads * 2);
 end
 
-mmcout=nargout;
-if(nargout>=3)
-    mmcout=nargout-1;
-    varargout{nargout}=cfg;
+mmcout = nargout;
+if (nargout >= 3)
+    mmcout = nargout - 1;
+    varargout{nargout} = cfg;
 end
 
-if(useopencl==1)
-    for i=1:length(cfg)
-        if(isfield(cfg(i),'gpuid') && ~ischar(cfg(i).gpuid) && cfg(i).gpuid<-1)
-	    cfg(i).gpuid=1;
+if (useopencl == 1)
+    for i = 1:length(cfg)
+        if (isfield(cfg(i), 'gpuid') && ~ischar(cfg(i).gpuid) && cfg(i).gpuid < -1)
+            cfg(i).gpuid = 1;
         end
     end
-    [varargout{1:mmcout}]=mmc(cfg);
-elseif(length(varargin)<2)
-    [varargout{1:mmcout}]=mmc(cfg);
-elseif(strcmp(type,'omp'))
-    [varargout{1:mmcout}]=mmc(cfg);
-elseif(strcmp(type,'sse'))
-    [varargout{1:mmcout}]=mmc_sse(cfg);
-elseif(strcmp(type,'prep') && nargout==1)
-    varargout{1}=cfg;
-elseif(strcmp(type,'preview') && nargout==1)
-    varargout{1}=mcxpreview(cfg);
+    [varargout{1:mmcout}] = mmc(cfg);
+elseif (length(varargin) < 2)
+    [varargout{1:mmcout}] = mmc(cfg);
+elseif (strcmp(type, 'omp'))
+    [varargout{1:mmcout}] = mmc(cfg);
+elseif (strcmp(type, 'sse'))
+    [varargout{1:mmcout}] = mmc_sse(cfg);
+elseif (strcmp(type, 'prep') && nargout == 1)
+    varargout{1} = cfg;
+elseif (strcmp(type, 'preview') && nargout == 1)
+    varargout{1} = mcxpreview(cfg);
 else
     error('type is not recognized');
 end
 
-if(mmcout>=2)
-    for i=1:length(varargout{2})
-        if(~isfield(cfg(i),'issaveexit') || cfg(i).issaveexit~=2)
-            medianum=size(cfg(i).prop,1)-1;
-            detp=varargout{2}(i).data;
-            if(isempty(detp))
-                continue;
+if (mmcout >= 2)
+    for i = 1:length(varargout{2})
+        if (~isfield(cfg(i), 'issaveexit') || cfg(i).issaveexit ~= 2)
+            medianum = size(cfg(i).prop, 1) - 1;
+            detp = varargout{2}(i).data;
+            if (isempty(detp))
+                continue
             end
-            newdetp.detid=int32(detp(1,:))';
-            newdetp.nscat=int32(detp(2:medianum+1,:))';    % 1st medianum block is num of scattering
-            newdetp.ppath=detp(medianum+2:2*medianum+1,:)';% 2nd medianum block is partial path
-            if(isfield(cfg(i),'ismomentum') && cfg(i).ismomentum)
-                newdetp.mom=detp(2*medianum+2:3*medianum+1,:)'; % 3rd medianum block is the momentum transfer
+            newdetp.detid = int32(detp(1, :))';
+            newdetp.nscat = int32(detp(2:medianum + 1, :))';    % 1st medianum block is num of scattering
+            newdetp.ppath = detp(medianum + 2:2 * medianum + 1, :)'; % 2nd medianum block is partial path
+            if (isfield(cfg(i), 'ismomentum') && cfg(i).ismomentum)
+                newdetp.mom = detp(2 * medianum + 2:3 * medianum + 1, :)'; % 3rd medianum block is the momentum transfer
             end
-            if(isfield(cfg(i),'issaveexit') && cfg(i).issaveexit)
-                newdetp.p=detp(end-6:end-4,:)';             %columns 7-5 from the right store the exit positions*/
-                newdetp.v=detp(end-3:end-1,:)';	     %columns 4-2 from the right store the exit dirs*/
+            if (isfield(cfg(i), 'issaveexit') && cfg(i).issaveexit)
+                newdetp.p = detp(end - 6:end - 4, :)';             % columns 7-5 from the right store the exit positions*/
+                newdetp.v = detp(end - 3:end - 1, :)';      % columns 4-2 from the right store the exit dirs*/
             end
-            newdetp.w0=detp(end,:)';  % last column is the initial packet weight
-            newdetp.prop=cfg(i).prop;
-            if(isfield(cfg(i),'unitinmm'))
-                newdetp.unitinmm=cfg(i).unitinmm;
+            newdetp.w0 = detp(end, :)';  % last column is the initial packet weight
+            newdetp.prop = cfg(i).prop;
+            if (isfield(cfg(i), 'unitinmm'))
+                newdetp.unitinmm = cfg(i).unitinmm;
             end
-            newdetp.data=detp;      % enable this line for compatibility
-            newdetpstruct(i)=newdetp;
+            newdetp.data = detp;      % enable this line for compatibility
+            newdetpstruct(i) = newdetp;
         else
-            newdetpstruct(i)=varargout{2}(i);
+            newdetpstruct(i) = varargout{2}(i);
         end
     end
-    if(exist('newdetpstruct','var'))
-        varargout{2}=newdetpstruct;
+    if (exist('newdetpstruct', 'var'))
+        varargout{2} = newdetpstruct;
     end
 end
 
@@ -496,6 +495,6 @@
     end
 end
 
-if(nargout>=4)
-    [varargout{3:end}]=deal(varargout{[end 3:end-1]});
+if (nargout >= 4)
+    [varargout{3:end}] = deal(varargout{[end 3:end - 1]});
 end
diff --git a/src/buildmmc.m b/src/buildmmc.m
index 3b40762b..19d7c0fa 100644
--- a/src/buildmmc.m
+++ b/src/buildmmc.m
@@ -3,8 +3,8 @@ function buildmmc(varargin)
 % Format:
 %    buildmmc or buildmmc('option1',value1,'option2',value2,...)
 %
-% Compiling script for mmclab mex file in MATLAB and GNU Octave. 
-% If compiled successfully, the output mex file can be found in the 
+% Compiling script for mmclab mex file in MATLAB and GNU Octave.
+% If compiled successfully, the output mex file can be found in the
 % mmc/mmclab folder (or ../mmclab using relative path from mmc/src)
 %
 % Author: Qianqian Fang <q.fang at neu.edu>
@@ -12,7 +12,7 @@ function buildmmc(varargin)
 % Input:
 %    options: without any option, this script compiles mmc.mex* using
 %    default settings. Supported options include
-%      'include': a string made of sequences of ' -I"/folder/path" ' that 
+%      'include': a string made of sequences of ' -I"/folder/path" ' that
 %            can be included for compilation (format similar to the -I
 %            option for gcc)
 %      'lib': a string made of sequences of ' -L"/folder/path" ' and '
@@ -22,8 +22,8 @@ function buildmmc(varargin)
 %
 % Dependency (Windows only):
 %  1.If you have MATLAB R2017b or later, you may skip this step.
-%    To compile mmclab in MATLAB R2017a or earlier on Windows, you must 
-%    pre-install the MATLAB support for MinGW-w64 compiler 
+%    To compile mmclab in MATLAB R2017a or earlier on Windows, you must
+%    pre-install the MATLAB support for MinGW-w64 compiler
 %    https://www.mathworks.com/matlabcentral/fileexchange/52848-matlab-support-for-mingw-w64-c-c-compiler
 %
 %    Note: it appears that installing the above Add On is no longer working
@@ -39,8 +39,8 @@ function buildmmc(varargin)
 %
 %       setenv('MW_MINGW64_LOC','C:\msys64\usr');
 %
-%  2.After installation of MATLAB MinGW support, you must type 
-%    "mex -setup C" in MATLAB and select "MinGW64 Compiler (C)". 
+%  2.After installation of MATLAB MinGW support, you must type
+%    "mex -setup C" in MATLAB and select "MinGW64 Compiler (C)".
 %  3.Once you select the MingW C compiler, you should run "mex -setup C++"
 %    again in MATLAB and select "MinGW64 Compiler (C++)" to compile C++.
 %  4.File C:\Windows\System32\OpenCL.dll must exist. You can obtain this
@@ -53,72 +53,72 @@ function buildmmc(varargin)
 %
 
 cd(fileparts(which(mfilename)));
-if(nargin==1 && strcmp(varargin{1},'clean'))
-    if(~isempty(dir('*.o')))
-        delete('*.o'); 
+if (nargin == 1 && strcmp(varargin{1}, 'clean'))
+    if (~isempty(dir('*.o')))
+        delete('*.o');
     end
-    return;
+    return
 end
-opt=struct(varargin{:});
-pname='mmc';
+opt = struct(varargin{:});
+pname = 'mmc';
 
 clsource = fileread('mmc_core.cl');
 clsrc = sprintf('0x%02x, ', char(clsource));
-clhex = ['unsigned char mmc_core_cl[] = {' sprintf('\n') clsrc(1:end-2) sprintf('\n')  ...
-    sprintf('};\nunsigned int mmc_core_cl_len = %d;\n', length(clsource))];
+clhex = ['unsigned char mmc_core_cl[] = {' sprintf('\n') clsrc(1:end - 2) sprintf('\n')  ...
+         sprintf('};\nunsigned int mmc_core_cl_len = %d;\n', length(clsource))];
 
-fp=fopen('mmc_core.clh','wb');
+fp = fopen('mmc_core.clh', 'wb');
 fwrite(fp, clhex, 'char');
 fclose(fp);
 
-cflags='-c -Wall -g -DMCX_EMBED_CL -fno-strict-aliasing -m64 -DMMC_USE_SSE -DHAVE_SSE2 -msse -msse2 -msse3 -mssse3 -msse4.1 -O3 -fopenmp  -DUSE_OS_TIMER -DUSE_OPENCL -DMCX_CONTAINER';
+cflags = '-c -Wall -g -DMCX_EMBED_CL -fno-strict-aliasing -m64 -DMMC_USE_SSE -DHAVE_SSE2 -msse -msse2 -msse3 -mssse3 -msse4.1 -O3 -fopenmp  -DUSE_OS_TIMER -DUSE_OPENCL -DMCX_CONTAINER';
 
-filelist={'mmc_rand_xorshift128p.c','mmc_mesh.c','mmc_raytrace.c',...
-    'mmc_utils.c','mmc_tictoc.c','mmc_host.c',...
-    'mmc_highorder.cpp','mmc_cl_utils.c','mmc_cl_host.c','mmclab.cpp'};
-if(isfield(opt,'filelist'))
-    filelist=opt.filelist;
+filelist = {'mmc_rand_xorshift128p.c', 'mmc_mesh.c', 'mmc_raytrace.c', ...
+            'mmc_utils.c', 'mmc_tictoc.c', 'mmc_host.c', ...
+            'mmc_highorder.cpp', 'mmc_cl_utils.c', 'mmc_cl_host.c', 'mmclab.cpp'};
+if (isfield(opt, 'filelist'))
+    filelist = opt.filelist;
 end
-if(isfield(opt,'include'))
-    cflags=[cflags ' ' opt.include];
+if (isfield(opt, 'include'))
+    cflags = [cflags ' ' opt.include];
 end
-if(ispc)
-    linkflags='$LINKLIBS -fopenmp -lstdc++ -static';
-    cflags=[cflags ' -I./mingw64/include -I"$MINGWROOT/opt/include"'];
-    linkflags=[linkflags ' ''C:\Windows\System32\OpenCL.dll'' '];
-    linkvar='LINKLIBS';
+if (ispc)
+    linkflags = '$LINKLIBS -fopenmp -lstdc++ -static';
+    cflags = [cflags ' -I./mingw64/include -I"$MINGWROOT/opt/include"'];
+    linkflags = [linkflags ' ''C:\Windows\System32\OpenCL.dll'' '];
+    linkvar = 'LINKLIBS';
 else
-    linkflags='\$LINKLIBS -fopenmp -static-libgcc -static-libstdc++';
-    cflags=[cflags ' -fPIC '];
-    linkflags=[linkflags ' -lOpenCL '];
-    linkvar='LINKLIBS';
+    linkflags = '\$LINKLIBS -fopenmp -static-libgcc -static-libstdc++';
+    cflags = [cflags ' -fPIC '];
+    linkflags = [linkflags ' -lOpenCL '];
+    linkvar = 'LINKLIBS';
 end
-if(~exist('OCTAVE_VERSION','builtin'))
-    for i=1:length(filelist)
-        flag='CFLAGS';
-        if(regexp(filelist{i},'\.[Cc][Pp][Pp]$'))
-            flag='CXXFLAGS';
+if (~exist('OCTAVE_VERSION', 'builtin'))
+    for i = 1:length(filelist)
+        flag = 'CFLAGS';
+        if (regexp(filelist{i}, '\.[Cc][Pp][Pp]$'))
+            flag = 'CXXFLAGS';
         end
-        disp(sprintf('mex OBJEXT=.o %s=''%s'' -c ''%s'' ',flag,cflags,filelist{i}));
-        eval(sprintf('mex OBJEXT=.o %s=''%s'' -c ''%s'' ',flag,cflags,filelist{i}));
+        disp(sprintf('mex OBJEXT=.o %s=''%s'' -c ''%s'' ', flag, cflags, filelist{i}));
+        eval(sprintf('mex OBJEXT=.o %s=''%s'' -c ''%s'' ', flag, cflags, filelist{i}));
     end
-    if(isfield(opt,'lib'))
-        linkflags=[linkflags ' ' opt.lib];
+    if (isfield(opt, 'lib'))
+        linkflags = [linkflags ' ' opt.lib];
     end
-    fn=dir('*.o');
-    fprintf(1,  'mex %s -output %s -outdir ../%slab %s=''%s''\n',strjoin({fn.name}),pname,pname,linkvar,linkflags);
-    eval(sprintf('mex %s -output %s -outdir ../%slab %s=''%s'' ',strjoin({fn.name}),pname,pname,linkvar,linkflags));
+    fn = dir('*.o');
+    fprintf(1,  'mex %s -output %s -outdir ../%slab %s=''%s''\n', strjoin({fn.name}), pname, pname, linkvar, linkflags);
+    eval(sprintf('mex %s -output %s -outdir ../%slab %s=''%s'' ', strjoin({fn.name}), pname, pname, linkvar, linkflags));
 else
-    linkflags=regexprep(linkflags,['[\\]*\$' linkvar],'');
-    for i=1:length(filelist)
-        cmd=sprintf('mex %s -c ''%s'' ',cflags,filelist{i});
-        fprintf(stdout,'%s\n',cmd);
-	fflush(stdout);
+    linkflags = regexprep(linkflags, ['[\\]*\$' linkvar], '');
+    for i = 1:length(filelist)
+        cmd = sprintf('mex %s -c ''%s'' ', cflags, filelist{i});
+        fprintf(stdout, '%s\n', cmd);
+        fflush(stdout);
         eval(cmd);
     end
-    fn=dir('*.o');
-    cmd=sprintf('mex %s -o ../%slab/%s %s ',strjoin({fn.name}),pname,pname,linkflags);
-    fprintf(1,'%s\n',cmd);
+    fn = dir('*.o');
+    cmd = sprintf('mex %s -o ../%slab/%s %s ', strjoin({fn.name}), pname, pname, linkflags);
+    fprintf(1, '%s\n', cmd);
     fflush(1);
     eval(cmd);
 end