Well, the $ctr = 0 doesn't do anything useful, and the $ctr += 1 could be merged into the if conditional.

my @converted_list = map { sprintf('0x%04x', $_) } unpack('v*', $line)
+;
    
my $ctr;
foreach (@converted_list) {
   print OUTFILE "$_, ";
   print OUTFILE "\n" unless ++$ctr % 8;
}
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You could merge of all that together if you so desired, but that's probably a bit odd.

my $ctr;
print map { ++$ctr % 8 ? "$_, " : "$_\n" }
      map { sprintf('0x%04x', $_) }
      unpack('v*', $line);
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The simplest solution is probably to omit the counter altogether by only reading in 16 bytes at a time. As a bonus, it doesn't leave trailing comma when the file isn't an exact multiple of 16 bytes long.

# Each line has 8 16-bit words, so 16 bytes.
local $/ = \16;

while (<INFILE>) {
   print join ', ',
         map { sprintf('0x%04x', $_) }
         unpack('v*', $_);
   print("\n");
}
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