Aug 212012
 
error_reporting(E_ALL);
ini_set('display_errors', '1');

// Load Up Magento Core
define('MAGENTO', realpath('/'));

require_once(MAGENTO . 'app/Mage.php');

$app = Mage::app();

$categories = Mage::getModel('catalog/category')
 ->getCollection()
 ->addAttributeToSelect('*')
 ->addAttributeToFilter('is_anchor', 0)
 ->addAttributeToFilter('entity_id', array("gt" => 1))
 ->setOrder('entity_id')
 ;

foreach($categories as $category) {
 echo $category->getId() . "\t" . $category->getName() . "\n";
 $category->setIsAnchor(1);
 $category->save();
}