I don't know the values of the variables you are using but this seems to work
n = 5;
k = rand(n,n);
sk = size(k)
k0 = 1:numel(k) %must be (maximum) the number of elements in k
ll = 1;
for i=1:sk(1)
for j=1:sk(2)
if k(i,j)>0.5
k1(i,j)=k(i,j);
else
k1(i,j)=k0(ll);
ll=ll+1;
end
end
end