PHP runs on the server and Javascript runs on the client, so you can't set a PHP variable to equal a Javascript variable without sending the value to the server. You can, however, set a Javascript variable to equal a PHP variable:
<script type="text/javascript">
var foo = '<?php echo $foo ?>';
</script>
To send a Javascript value to PHP you'd need to use AJAX. With jQuery, it would look something like this (most basic example possible):
var variableToSend = 'foo';
$.post('file.php', {variable: variableToSend});
On your server, you would need to receive the variable sent in the post:
$variable = $_POST['variable'];