Vertex Sorting of 3D Images

The problem I am dealing with is that I am taking the image data from two 2D images (MRI scans) and to determine which points on the lower slice correspond to the points on the upper slice, then ordering them in order to form a mesh enclosing the boundaries of the image.

 for j=1:size(Old_Slice,1)
% Old Slice refers to the Upper slice while Vertices refers to the upper slice
            GPx=abs(Old_Slice(j,1)-Vertices(:,1));
            GPy=abs(Old_Slice(j,2)-Vertices(:,2));
            GP=[GPx GPy];
            [val,idx]=min(sum(GP,2));
            % Setting a minimum value of how close the two points of the images must be
            if val<0.5
                if lag==0
                    k=1;
                    lag=2;
                end
                order(k)=idx;
                k=k+1;
            end
        end
        k=1;
        % Attempting to order the Vertexes so they follow the right order to plot
        while k<min([size(Old_Slice,1) size(order,2)])
            NData(2*k-1,:)=[Old_Slice(k,:) (i-1)/10];
            NData(2*k,:)=[Vertices(order(k),:) i/10];
            k=k+1;
        end

The main issue comes in that when I try to order the vertexes of the two images so that I can plot them in the sequential order it works for about half of the data points but not all.