gistfile1.txt

<?php
try {
    error_reporting(E_ALL);
    ini_set('display_errors', '1');

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

    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();
    }
    print "If your seeing this there were no errors.";
}
catch (Exception $e) {
  print "OOOPS! " . $e->getMessage() . "\n";
}