Actually, your code has a number of problems.

• that isn't how you initialize a 2-dimensional array. your initialization of @matrix will make a 722 element 1d array. You would need something like: @matrix=map {[(0) x 361]} (0..361);
• From what I can see you want:  $Matrix[$a+180][$b+180] += 1;

I would suggest giving Modern Perl or Learning Perl and Programming Perl a good read to get down some of the fundamentals.

Update: Also you set $a and $b to values, then immediately set them to int($phi) and int($psi) which are undefined. If you were running with strict and warnings the compiler would have shown you that.