Hi Damith - I'd go with a double for loop, pre-allocating memory for the X and Y vectors:
[m,n] = size(matrix1); % where matrix1 is the 39x39 matrix
numElems = (m-1)*m/2; % since ignoring elements on matrix diagonal
X = zeros(numElems,1);
Y = X;
at = 1;
for i=1:m
for j=i+1:m % since not interested in i==j
X(at) = matrix1(j,i);
Y(at) = matrix1(i,j);
at = at + 1;
end
end
