Here is what I sometimes tell my younger children on those infrequent occasions when they wake up in the middle of the night terrified after a nightmare — especially if the experience makes them feel unprotected by God or their guardian angel.

“I know it seems like bad dreams are something bad that just happens to you. But I think most dreams, good or bad, are like stories that we tell ourselves — stories that a part of your brain tells to another part of your brain. Sometimes good stories, sometimes scary stories … but stories we make up ourselves, with a different part of our brain. And I think that part of us usually knows what it’s doing — and God knows that. Maybe being scared in a dream helps you to be braver when bad things happen in the real world. But now that the dream is over, you don’t have to worry about having it again. You won’t; I promise. You’ll see in the morning.”

Something like that seems the right place to begin with Coraline, a dark fantasy with surreal elements that feel like a story that a little girl tells herself, initially for comfort and amusement, until the disquieting elements take over and the dream becomes a nightmare. Even then, though, there are signs that the little girl is still ultimately in control, still telling the story herself.

Fantasy writer Neil Gaiman says his 2002 novella Coraline was in fact built around key themes from stories that his daughter Holly made up when she was 4 or 5 years old — stories about a girl named Holly whose mother gets kidnapped by a witch that resembles the mother. Why would a little girl invent such a theme? Where does that come from? A part of the brain that knows what it’s doing, I suspect.

The choice of stop-motion animation for the big-screen version of Coraline is an inspired one for a story that involves an uncanny rag doll with button eyes that bears a striking resemblance to the young protagonist. Dolls, like clowns and carousels, can be charming or magical, but the possibility for creepiness is always just around the corner.

Likewise, stop-motion animation, which involves photographing articulated figures — dolls — one frame at a time, making tiny movements between shots to create the illusion of movement, can be delightful, like Aardman’s Wallace & Gromit and “Shaun the Sheep” (see “DVD Picks”), or matter-of-factly miraculous, like The Miracle Maker.

Still, the technique seems well-suited to creepiness: Witness Tim Burton’s Corpse Bride, as well as the previous efforts of Coraline writer-director Henry Selick, The Nightmare Before Christmas and James and the Giant Peach. (Is it a coincidence that even Wallace and Gromit’s adventures usually take the form of spoofs of thriller/horror films?)

Although the discovery of a parallel world accessed through a magical portal in her parents’ new home is where the weirdness really gets started for young Coraline (voiced by Dakota Fanning), it’s the haunting stop-motion magic of her own world that opens the door to the magic of that other world.

In a dreamlike way, Coraline is intrigued, but not totally freaked out, by the nocturnal discovery of an alternate version of her home, a ramshackle Victorian house with attic and basement apartments, where she meets surreal counterparts of her parents (voiced in both worlds by Teri Hatcher and John Hodgman), the eccentric upstairs and downstairs neighbors, and neighborhood boy Wybie (Robert Bailey Jr.), whose aunt owns the house Coraline’s parents and neighbors are renting.

Even the nightmarish twist that these alternate-world residents, who otherwise look pretty much like the real thing, have sewn button eyes like Coraline’s rag doll in lieu of real eyes doesn’t send Coraline screaming back to the real world — a sure mark of the dream logic of her adventures.

In fact, doll eyes notwithstanding, Coraline is rather taken with this alternate world, which, in many ways, she finds preferable to her humdrum real-world life.

Her real parents, both writers, are too swamped with work to pay attention to Coraline or even keep the fridge stocked. By contrast, the Other Mother seems warmly solicitous and cheerily domestic, preparing lavish feasts for Coraline’s visits (in a typically unsettling touch, the parents don’t touch the food themselves), while the Other Father whimsically whiles away his time at a piano.

But if the eyes are the windows of the soul, a world of people with doll-like sewn button eyes can’t be wholesome — and presently, Coraline becomes aware of the sinister agenda underlying the Other Mother’s sweet demeanor. (Even in the real world, Coraline’s father calls her mother “the boss.”)

Although Coraline eventually affirms Coraline’s real parents over her fantasy ones, the film waits too long to attempt the parents’ redemption, and the ending comes off as rote and not really earned (a little like the romantic final scene of The Nightmare Before Christmas). A better film might have humanized the parents more throughout the film, perhaps mitigating their unavailability with more conflict and evident affection for Coraline.

Perhaps, too, Coraline might have been allowed some petulance and room to grow.

As scary as things get, Coraline is never completely overwhelmed. A savvy cat that travels between both worlds (Keith David) acts as an anchor, and from the moment Coraline challenges the Other Mother to a game, it’s clear who’s really in charge.

For stop-motion auteur Selick, Coraline is a technical triumph. The most ambitious and sophisticated stop-motion film ever created, Coraline is filmed in stereoscopic 3-D (look for a theater offering the 3-D experience), with an unprecedented range of complexity and expressive nuance comparable to computer animation.

At 100 minutes, Coraline feels a little longer than it needs to, though it’s never boring, and its beguiling world is so lovingly realized that you understand Selick’s reluctance to leave it. With its dark tale of changeling parents and captured souls, it comes closer to the spirit of the traditional European fairy tale than almost any other film, animated or otherwise, in recent memory.

Steven D. Greydanus is editor

and chief critic at DecentFilms.com.

Content advisory: Creepy imagery, scary scenes and menace to a child; disturbing domestic themes in a fantasy setting; a couple of instances of divination (dowsing, tea leaves); mild burlesque-style humor. Too scary for many children.