you have a bit of an issue with the command order...
it needs to be:
convert -thumbnail '100x100>' input.jpg output.gif
I used your coding to make this php script.. it does nothing but resize the image hardcoded into the script... the code is as follows:
CODE
<?php
$imagemagickPath = "/usr/local/bin";
system("$imagemagickPath/convert -thumbnail '100x100>' input.jpg output.gif");
exit;
?>
You can see it work here:
http://www.pr0ntab.com/kingtaco/