What I did was try a few different nested loops (counter), and compare the numbers to yours (what you typed)

It took like 8 permutations to get the numbers to match

sub makeRatio { 
    my( $d_h ) = @_;
    my $rows    =  $#$d_h ; ## last index of array
    my $columns =  $#{ $d_h->[0] }; ## last index of first row
    my @ratio;
    for my $six ( 0 .. $columns ){
        for my $tre ( 0 .. $rows ){
            for my $tri ( 0 .. $rows ){
                ## for visual matching
                printf 'my $ratio%d_%d_%d  = $$d_h[%d][%d] / $$d_h[%d]
+[%d];'."\n",
                    1+$six, 1+$tri, 1+$tre,
                    $tri, $six,
                    $tre, $six,
                    ;;;
                $ratio[ $six ][ $tri ][ $tre ] = $$d_h[ $tri ][ $six ]
+ / $$d_h[ $tre ][ $six ] ;
            }
        }
    }
    return \@ratio ;
}
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Naturally this is 0 indexed since programmers count from 0 (I was not tempted to change $ARRAY_BASE )

Then I turned more of your stuff into arrays slowly so that when writing functions I can compare/verify numbers .... should have done 2 rows 2 colums, whew :)

Now it wasn't too huge of a deal to compare what you got (what is expected) with what I got using my eyes, but once you come up with a function like I did, you should write a test for it, ...