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my @matrix=([qw(1 2 4 4)],[qw(5 2 0 8)],[qw(9 10 11 12)],);

...
    $t[$i][$j] = $matrix[$j][$i];
  }
}

$VAR1 = [
          [ 1, 5, 9 ],
...
          [ 4 ],
          [ 4, 8, 12 ],
        ]