Take a look into the two link might solve the problem if you did with enqueue standards you might solve jquery conflict. http://codex.wordpress.org/Function_Reference/wp_register_script
http://codex.wordpress.org/Function_Reference/wp_enqueue_script
Create a script.js file
$(window).load(function() {
$('#slider').nivoSlider();
});
Open your theme file functions.php and add the below code:
create function
function enqueue_script_for_nivo () {
wp_enqueue_script('jquery');
// Load your nivo script too here.
wp_register_script('nivoscript',get_stylesheet_directory_uri().'/bootstrap/js/jquery.nivo.slider.pack.js"');
wp_register_script( 'my-script', get_stylesheet_directory_uri() . '/js/script.js' );
wp_enqueue_script('nivoscript');
wp_enqueue_script('my-script');
}
add_action('wp_enqueue_scripts','enqueue_script_for_nivo');
That's all try this one hopefully it should work :)