John,

While it would be more helpful, if you could post what errors, if any,
you are getting, right off the top of my head I would suggest you take
a look at your system() call.

system("convert -geometry ".$size."x".$size."-quality
$qual $file".$prefix."$file");
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Now I'll give you that you probably split the line to make it easier to
read in your post, however, the statement is probably not passing a
valid command to the shell. For example, if

$file = "someimage.jpeg";
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at some point in the loop, then the system() will be called with the string

convert -geometry 100x100-quality 50 someimage.jpegtn_someimage.jpeg
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Check your spacing and see if that fixes your problem.