Nowinski and Thaung Brain Inf. (2018) 5:1 https://doi.org/10.1186/s40708-018-0082-1 Brain Informatics ORIGINAL RESEARCH Open Access A 3D stereotactic atlas of the adult human skull base Wieslaw L. Nowinski1,2* and Thant S. L. Thaung3 Abstract Background: The skull base region is anatomically complex and poses surgical challenges. Although many textbooks describe this region illustrated well with drawings, scans and photographs, a complete, 3D, electronic, interactive, real- istic, fully segmented and labeled, and stereotactic atlas of the skull base has not yet been built. Our goal is to create a 3D electronic atlas of the adult human skull base along with interactive tools for structure manipulation, exploration, and quantifcation. Methods: Multiple in vivo 3/7 T MRI and high-resolution CT scans of the same normal, male head specimen have been acquired. From the scans, by employing dedicated tools and modeling techniques, 3D digital virtual models of the skull, brain, cranial nerves, intra- and extracranial vasculature have earlier been constructed. Integrating these models and developing a browser with dedicated interaction, the skull base atlas has been built. Results: This is the frst, to our best knowledge, truly 3D atlas of the adult human skull base that has been created, which includes a fully parcellated and labeled brain, skull, cranial nerves, and intra- and extracranial vasculature. Conclusion: This atlas is a useful aid in understanding and teaching spatial relationships of the skull base anatomy, a helpful tool to generate teaching materials, and a component of any skull base surgical simulator. Keywords: Skull base, Electronic atlas, Digital models, Skull, Brain, Stereotactic atlas 1 Introduction carotid arteries, among others. Moreover, the skull base Te base of skull, or skull base, forms the foor of the provides access to hardly accessible intracranial lesions cranial cavity and separates the brain from other struc- located adjacent to the brainstem [1]. Terefore, knowl- tures of the face and neck. It is composed of fve bones: edge of the normal and variant anatomy of the skull base ethmoid, sphenoid, occipital, frontal, and paired tem- is essential for efective surgical treatment of disease in poral. Te skull base is subdivided into three distinct this region. regions called fossae: the anterior, middle, and posterior Te skull base has been comprehensively described in cranial fossae. Te base of skull not only separates the many textbooks [2–4], Gray’s anatomy [5–7], and print intracranial content and the facial compartment from the atlases [1, 8, 9]. Tis kind of material is illustrated with upper respiratory and digestive tracts, but it also enables drawings, tomographic scans and pictures of cadaveric the passage of vital neurovascular structures entering and specimens where the images are typically unlabeled. exiting the brain. Te skull base region is anatomically Te skull base region is also available in some electronic complex and poses surgical challenges for neurosurgeons atlases of the head and neck [10–14]. Tese applications and otolaryngologists because of proximity to important vary from medical illustrations to animations to lim- structures, such as the brain, cranial nerves, orbits, and ited three-dimensional (3D) models. Another approach enabling to study the skull base region is to generate 3D printed models [15]. Moreover, some applications *Correspondence: [email protected]; [email protected] 1 John Paull II Center for Virtual Anatomy and Surgical Simulation, Cardinal employ virtual reality systems for training and planning Stefan Wyszynski University, Woycickiego 1/3, Block 12, Room 1220, skull base surgery [15, 16]. 01‑938 Warsaw, Poland Full list of author information is available at the end of the article © The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creat​iveco​mmons​.org/licen​ses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Nowinski and Thaung Brain Inf. (2018) 5:1 Page 2 of 9 Although many textbooks describe the skull base carefully processed to ft the blood vessels and cranial region well illustrated with drawings, scans, and photo- nerves that pass in and out of them. graphs of anatomical dissections as well as animations Te brain model was constructed from a 3 T and other electronic media have been developed for magnetization-prepared rapid gradient echo (MP- studying the skull base region, a complete, truly 3D, elec- RAGE) scan with a 224 300 320 resolution and a 3 × × tronic, interactive, realistic, fully segmented and labeled, 0.8 × 0.8 × 0.8 mm voxel size. Te brain was segmented decomposable, and stereotactic atlas of the skull base has by means of a dedicated contour editor, a 3D model con- not been created yet. Terefore, there is a great need for structed, and the cortex parcellated into lobes, gyri, and a 3D atlas covering the practical neuroanatomy of the sulci [18]. skull base region. Te goal of this work is to create a 3D In order to build a 3D model of the intracranial vascula- electronic atlas of the adult human skull base along with ture, multiple 3 and 7 T magnetic resonance angiography interactive tools for structure manipulation, exploration (MRA) scans were acquired, including 3D time of fight navigation, and quantifcation. (the main sequence with a 384 320 272 resolution 3 × × and a 0.52 × 0.52 × 0.5 mm voxel size), spoiled gradient 2 Materials and methods recovery, and susceptibility weighted imaging. Te ves- A 3D atlas of the adult human skull base region has been sels were extracted using a dedicated vascular editor [24] created from 3D digital virtual models of the skull, brain, and modeled as tubes as explained in [25]. Te vascular cranial nerves, intracranial vasculature, and extracranial editor provides functions for a rapid extraction of vessels vasculature. Tese models have been built earlier from on the orthogonal axial, coronal, and sagittal planes and in vivo multiple 3 and 7 Tesla (T) magnetic resonance constructing centerline and 3D polygonal tubular surface imaging (MRI) and high-resolution computed tomogra- models. phy (CT) scans of the same normal, male head specimen. Te extracranial vasculature was created in a simi- Te models have been incorporated into the 3D stereo- lar way from the same MRA scans as the intracranial tactic atlases of the skull [17], brain [18], cranial nerves vasculature and additionally from a 3D phase contrast [19], intracranial vasculature [20], and extracranial vas- MRA neck scan with a 352 352 261 matrix and a ×3 × culature [21]. 0.568182 × 0.568182 × 1.0 mm voxel size [21]. A process of anatomical model building was, generally, Te cranial nerves (CN) extracted initially by means of similar for each model, although varying in data acqui- the vascular editor from the MP-RAGE scan were also sition, modeling methods, building suitable tools, and modeled as tubes, and further extended and fne-tuned validation. Tis process included the following steps: as described in [19]. Te CN model contains all 12 pairs in vivo scan acquisition, scan segmentation, scan parcel- of CN I-XII (with over 600 segments) as listed in [19]. lation into individual structures, 3D surface modeling, In order to browse, explore, navigate, quantify, and 3D model simplifcation (decimation or compressing), 3D manipulate the skull base models, the atlas is equipped surface editing, 3D model color-coding, 3D object nam- with a user-friendly browser with dedicated interaction. ing based on Terminologia Anatomica [22], and model Browsing and exploration is facilitated by: (1) the assem- validation. Te anatomical models were placed in the bling (compositing) and disassembling (decompositing) Talairach stereotactic coordinate system [23], and a read- mechanism with an individual and group selection allow- out of distances and the stereotactic coordinates (pos- ing the investigator to build any region of interest or (sub) terior–anterior, inferior–superior, and right–left) were system and to present a local anatomy within its global provided. context; (2) virtual brain dissections in seven directions In order to build a 3D model of the skull, a high-resolu- to see through the brain; (3) real-time structure and scan tion spiral CT scan was acquired with 526 axial slices of manipulation; (4) 3D labeling of surface and sectional 0.75 mm thickness, 0.5 mm increment, 512 512 matrix MRI anatomy; (5) structure highlighting, (6) interaction 2 × and 0.46875 × 0.46875 mm pixel size. Te skull was orig- combined with animation; and (7) quantifcation with a inally parcellated into 29 individual bones, reconstructed readout of distances, vessel diameters, and the stereotac- in 3D, and validated as featured in [17]. Te skull was tic coordinates. also cut anterio-posteriorly with its superior part remov- able in order to enable exposure of the skull base region. 3 Results Te 3D skull base model comprises 5 bones: ethmoid, Te 3D, electronic and stereotactic atlas of the adult sphenoid, occipital, frontal, and paired temporal, as well human skull base has been designed and constructed as foramina and canals of the skull base and other bony and is illustrated in Figs. 1, 2, 3, 4, 5, 6, 7, 8, and 9. structures along with landmarks typical to this region. Te content of the atlas is listed in Appendix. Fig- Te size and shape of the foramina and canals were ure 1 shows the internal (superior view) and external Nowinski and Thaung Brain Inf. (2018) 5:1 Page 3 of 9 Fig. 2 Internal surface of the skull base labeled with: a anterior, middle and posterior fossa; b color-coded fve bones Fig.