ENH: Added all new repository files from local repository with NM code.

compute/compute_BMD.m

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+% This function compute the Bundle-based Minimum Distance (BMD) between two bundles [Garyfallidis et al, 2015]
+function [ distance ] = compute_BMD(bA, bB, Npoints)
+% bA: Bundle A (set of fibers)
+% bB: Bundle B (set of fibers)
+% Npoints: Number of points used to interpolate fibers ([Garyfallidis et al, 2015] uses Npoints=20)
+% distance: Bundle-based Minimum Distance (BMD) computed as in eq. (1) in [Garyfallidis et al, 2015]
+
+I = size(bA,1);
+J = size(bB,1);
+
+% Interpolate bundles
+bA = interpolate(bA,Npoints);
+bB = interpolate(bB,Npoints);
+
+vA = zeros(I,1);
+vB = zeros(J,1);
+
+% fix one fiber in Bundle A and compute the distances to every fibers in
+% Bundle B
+for i=1:I
+    disp(['across bA:',num2str(100*i/I),'%'])
+    fA = bA{i};
+    parfor j=1:J
+        vB(j) = MDF(fA,bB{j});
+    end
+    vA(i) = min(vB);
+end
+dA = mean(vA);
+
+% fix one fiber in Bundle B and compute the distances to every fibers in
+% Bundle A
+for j=1:J
+    disp(['across bB:',num2str(100*j/J),'%'])
+    fB = bB{j};
+    parfor i=1:I
+        vA(i) = MDF(bA{i},fB);
+    end
+    vB(j) = min(vA);
+end
+dB = mean(vB);
+
+distance = (dA + dB)/4;
+
+end
+
+% Function that provides an interpolated bundle with a constant N number of
+% points each fiber
+function [b] = interpolate(b,N)
+
+parfor f=1:size(b,1)
+    % Interpolate using Splines Tensor Toolbox
+    CS=cscvn(b{f}); % obtain spline model from points
+    t_range = linspace(CS.breaks(1),CS.breaks(end),N); % define range of t parameter in order to provide N points
+    b{f} = fnval(CS,t_range); % Evaluate curve at N points
+end
+
+end
+
+% Function that compute the Minimum average Direct-Flip (MDF) as defined in
+% eq. (2) in [Garyfallidis et al, 2015]
+function [dist] = MDF(f1,f2)
+N = size(f1,2);
+d_dir = mean(sqrt(sum((f1'-f2').^2,2)));
+d_flip = mean(sqrt(sum((f1'-flip(f2',1)).^2,2)));
+
+dist = min(d_dir,d_flip);
+
+end
+

compute/compute_BMD.m~

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+% This function compute the Bundle-based Minimum Distance (BMD) between two bundles [Garyfallidis et al, 2015]
+function [ distance ] = compute_BMD(bA, bB, Npoints)
+% bA: Bundle A (set of fibers)
+% bB: Bundle B (set of fibers)
+% Npoints: Number of points used to interpolate fibers ([Garyfallidis et al, 2015] uses Npoints=20)
+% distance: Bundle-based Minimum Distance (BMD) computed as in eq. (1) in [Garyfallidis et al, 2015]
+
+I = size(bA,1);
+J = size(bB,1);
+
+% Interpolate bundles
+bA = interpolate(bA,Npoints);
+bB = interpolate(bB,Npoints);
+
+vA = zeros(I,1);
+vB = zeros(J,1);
+
+% fix one fiber in Bundle A and compute the distances to every fibers in
+% Bundle B
+for i=1:I
+    disp(['across bA:',num2str(100*i/I),'%'])
+    fA = bA(:,i);
+    parfor j=1:J
+        vB(j) = MDF(fA,bB(:,j));
+    end
+    vA(i) = min(vB);
+end
+dA = mean(vA);
+
+% fix one fiber in Bundle B and compute the distances to every fibers in
+% Bundle A
+for j=1:J
+    disp(['across bB:',num2str(100*j/J),'%'])
+    fB = bB(:,j};
+    parfor i=1:I
+        vA(i) = MDF(bA{i},fB);
+    end
+    vB(j) = min(vA);
+end
+dB = mean(vB);
+
+distance = (dA + dB)/4;
+
+end
+
+% Function that provides an interpolated bundle with a constant N number of
+% points each fiber
+function [bout] = interpolate(b,N)
+bout = zeros(N,size(b,1));
+parfor f=1:size(b,1)
+    % Interpolate using Splines Tensor Toolbox
+    CS=cscvn(b{f}); % obtain spline model from points
+    t_range = linspace(CS.breaks(1),CS.breaks(end),N); % define range of t parameter in order to provide N points
+    bout(:,f) = fnval(CS,t_range); % Evaluate curve at N points
+end
+
+end
+
+% Function that compute the Minimum average Direct-Flip (MDF) as defined in
+% eq. (2) in [Garyfallidis et al, 2015]
+function [dist] = MDF(f1,f2)
+N = size(f1,2);
+d_dir = mean(sqrt(sum((f1'-f2').^2,2)));
+d_flip = mean(sqrt(sum((f1'-flip(f2',1)).^2,2)));
+
+dist = min(d_dir,d_flip);
+
+end
+

compute/compute_BMD_new.m

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+% This function compute the Bundle-based Minimum Distance (BMD) between two bundles [Garyfallidis et al, 2015]
+function [ distance ] = compute_BMD_new(bA, bB, Npoints)
+% bA: Bundle A (set of fibers)
+% bB: Bundle B (set of fibers)
+% Npoints: Number of points used to interpolate fibers ([Garyfallidis et al, 2015] uses Npoints=20)
+% distance: Bundle-based Minimum Distance (BMD) computed as in eq. (1) in [Garyfallidis et al, 2015]
+%parpool('local',12)
+
+I = size(bA,1);
+J = size(bB,1);
+
+% Interpolate bundles
+bA = interpolate(bA,Npoints);
+bB = interpolate(bB,Npoints);
+
+vA = zeros(I,1);
+% fix one fiber in Bundle A and compute the distances to every fibers in
+% Bundle B
+parfor i=1:I
+    %disp(['across bA:',num2str(100*i/I),'%'])
+    fA = repmat(bA(:,:,i),[1,1,J]);
+    vB1 = MDF_block(fA,bB);
+
+    vA(i) = min(vB1);
+end
+dA = mean(vA);
+
+vB = zeros(J,1);
+% fix one fiber in Bundle B and compute the distances to every fibers in
+% Bundle A
+parfor j=1:J
+    %disp(['across bB:',num2str(100*j/J),'%'])
+    fB = repmat(bB(:,:,j),[1,1,I]);
+    vA1 = MDF_block(fB,bA);
+
+    vB(j) = min(vA1);
+end
+dB = mean(vB);
+
+distance = (dA + dB)/4;
+
+end
+
+% Function that provides an interpolated bundle with a constant N number of
+% points each fiber
+function [bout] = interpolate(b,N)
+Nf = size(b,1);
+bout = zeros(3,N,Nf);
+%lengths_b = zeros(Nf,1);
+
+parfor f=1:Nf
+    % Interpolate using Splines Tensor Toolbox
+    CS=cscvn(b{f}); % obtain spline model from points
+    t_range = linspace(CS.breaks(1),CS.breaks(end),N); % define range of t parameter in order to provide N points
+    bout(:,:,f) = fnval(CS,t_range); % Evaluate curve at N points
+    %lengths_b(f) = size(b{f},2);
+end
+
+end
+
+% Function that compute the Minimum average Direct-Flip (MDF) as defined in
+% eq. (2) in [Garyfallidis et al, 2015]
+function [dist] = MDF(f1,f2)
+N = size(f1,2);
+d_dir = mean(sqrt(sum((f1'-f2').^2,2)));
+d_flip = mean(sqrt(sum((f1'-flip(f2',1)).^2,2)));
+
+dist = min(d_dir,d_flip);
+
+end
+
+function [dist] = MDF_block(f1,f2)
+
+d_dir = mean(sqrt(sum((f1-f2).^2,1)));
+d_flip = mean(sqrt(sum((f1-flip(f2,2)).^2,1)));
+
+dist = min([d_dir,d_flip],[],2);
+
+end
+

compute/compute_incoherence.m

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+% This function compute the Bundle-based Minimum Distance (BMD) between two bundles [Garyfallidis et al, 2015]
+function [ incoherence ] = compute_incoherence(bA, Npoints)
+% bA: Bundle A (set of fibers)
+% bB: Bundle B (set of fibers)
+% Npoints: Number of points used to interpolate fibers ([Garyfallidis et al, 2015] uses Npoints=20)
+% distance: Bundle-based Minimum Distance (BMD) computed as in eq. (1) in [Garyfallidis et al, 2015]
+
+I = size(bA,1);
+J = I;
+
+% Interpolate bundles
+bA = interpolate(bA,Npoints);
+bB = bA;
+
+vA = zeros(I,1);
+vB = zeros(J,1);
+
+% fix one fiber in Bundle A and compute the distances to every fibers in
+% Bundle B
+for i=1:I
+    i
+    fA = bA{i};
+    parfor j=1:J
+        if j~=i
+            vB(j) = MDF(fA,bB{j});
+        else
+            vB(j) = NaN;
+        end
+    end
+    vA(i) = min(vB);
+end
+
+
+incoherence = vA/2;
+
+end
+
+% Function that provides an interpolated bundle with a constant N number of
+% points each fiber
+function [b] = interpolate(b,N)
+
+parfor f=1:size(b,1)
+    % Interpolate using Splines Tensor Toolbox
+    CS=cscvn(b{f}); % obtain spline model from points
+    t_range = linspace(CS.breaks(1),CS.breaks(end),N); % define range of t parameter in order to provide N points
+    b{f} = fnval(CS,t_range); % Evaluate curve at N points
+end
+
+end
+
+% Function that compute the Minimum average Direct-Flip (MDF) as defined in
+% eq. (2) in [Garyfallidis et al, 2015]
+function [dist] = MDF(f1,f2)
+N = size(f1,2);
+d_dir = mean(sqrt(sum((f1'-f2').^2,2)));
+d_flip = mean(sqrt(sum((f1'-flip(f2',1)).^2,2)));
+
+dist = min(d_dir,d_flip);
+
+end
+

compute/compute_wBMD.m

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+% This function compute the weighted Bundle-based Minimum Distance (wBMD)
+% between two bundles. The wBMD is a modified BMD [Garyfallidis et al,
+% 2015] that takes into account the fiber weights assigned in LiFE.
+function [ distance ] = compute_wBMD(bA, bB, wA, wB, Npoints)
+% bA: Bundle A (set of fibers)
+% bB: Bundle B (set of fibers)
+% wA: weights for Bundle A
+% wB: weights for Bundle B
+% Npoints: Number of points used to interpolate fibers ([Garyfallidis et al, 2015] uses Npoints=20)
+% distance: Bundle-based Minimum Distance (BMD) computed as in eq. (1) in [Garyfallidis et al, 2015]
+
+I = size(bA,1);
+J = size(bB,1);
+
+% Interpolate bundles
+bA = interpolate(bA,Npoints);
+bB = interpolate(bB,Npoints);
+
+vA = zeros(I,1);
+vB = zeros(J,1);
+
+% normalize weights
+wA = wA./sum(wA);
+wB = wB./sum(wB);
+
+% fix one fiber in Bundle A and compute the distances to every fibers in
+% Bundle B
+for i=1:I
+    fA = bA{i};
+    parfor j=1:J
+        vB(j) = MDF(fA,bB{j});
+    end
+    vA(i) = min(vB);
+end
+dA = sum(wA.*vA);
+
+% fix one fiber in Bundle B and compute the distances to every fibers in
+% Bundle A
+for j=1:J
+    fB = bB{j};
+    parfor i=1:I
+        vA(i) = MDF(bA{i},fB);
+    end
+    vB(j) = min(vA);
+end
+dB = sum(wB.*vB);
+
+distance = (dA + dB)/4;
+
+end
+
+% Function that provides an interpolated bundle with a constant N number of
+% points each fiber
+function [b] = interpolate(b,N)
+
+parfor f=1:size(b,1)
+    % Interpolate using Splines Tensor Toolbox
+    CS=cscvn(b{f}); % obtain spline model from points
+    t_range = linspace(CS.breaks(1),CS.breaks(end),N); % define range of t parameter in order to provide N points
+    b{f} = fnval(CS,t_range); % Evaluate curve at N points
+end
+
+end
+
+% Function that compute the Minimum average Direct-Flip (MDF) as defined in
+% eq. (2) in [Garyfallidis et al, 2015]
+function [dist] = MDF(f1,f2)
+N = size(f1,2);
+d_dir = mean(sqrt(sum((f1'-f2').^2,2)));
+d_flip = mean(sqrt(sum((f1'-flip(f2',1)).^2,2)));
+
+dist = min(d_dir,d_flip);
+
+end
+