I have found a better way to do this that actually works. It is to use $image->copy($sourceImage,$dstX,$dstY,$srcX,$srcY,$width,$height)

#!/usr/bin/perl 

use GD;

use CGI::Carp qw/ fatalsToBrowser /;

use warnings;

print "Content-type: text/html\n\n";

$code_image_file = '8_QB.jpg';

$file_code = "$code_image_file";

$image_code = GD::Image->newFromJpeg($file_code);

$ESP_code = new GD::Image(200,200);

$ESP_code->copy($image_code,0,0,600,400,200,200);  

# Convert the image to JPEG and write it to a file.
$image =  $ESP_code->jpeg([50]);

binmode STDOUT;

#Write to file

open ESP_IMAGE, ">filepath/image.jpg";
print ESP_IMAGE $image;
close ESP_IMAGE;

print "<img src='image.jpg'>";
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