Tyrannosaurus rex Osborn 1905
Creators: name: Reims N
name: Schulp A
name: Bohnel M
name: Larson P
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Reptilia
Dinosauria
Tyrannosauridae
Tyrannosaurus
Tyrannosaurus rex

description: The 13 m long carnivorous dinosaur Tyrannosaurus rex is arguably the dinosaur best known by the general public (Brochu, 2003).  
With a new dinosaur gallery scheduled to open in 2018, the national natural history museum of the Netherlands, Naturalis Biodiversity Center, in Leiden, set out to acquire an original skeleton of this dinosaur. A skeleton of Tyrannosaurus rex was discovered in Spring and excavated in the Fall of 2013, from a sandstone stream channel of the Hell Creek Formation near Jordan, Montana, USA. The excavation relied upon a close collaboration between Black Hills Institute and Naturalis (Schulp et al., 2015). Reasonably complete skeletons of Tyrannosaurus are few and far between, and so far only two skeletons substantially more than 50% complete have been found (Larson & Carpenter, 2008). At the moment of submission of the present paper (March 2016), the Naturalis T. rex skeleton is still being prepared, and is currently scheduled to go on public display in Leiden in September 2016, where it is registered under collection number RGM 792.000. The specimen comprises a well-preserved skull, partial cervical and dorsal vertebral series, an almost-complete rib-cage, scapula-coracoid, furcula, a complete pelvis, the right leg, and about half of the tail. Probably no other innovation has had a similarly profound impact on the study of fossil vertebrates in the last few decades than the increased accessibility and improvement in image quality of CT scanning (e.g., Leiggi & May, 2003). The nondestructive character of CT allows for features otherwise inaccessible, to be visualized, described, compared and analyzed (Mallison, 2011; Abel et al., 2012). Medical CTscanners, with a bore suited to fit most humans, and, occasionally, veterinary CT scanners with a larger bore, now routinely allow for scanning of human-sized objects; however, the specifications of those imaging systems are optimized for objects less dense than fossils, and the X-ray performance is dimensioned for X-ray exposures “as low as reasonably achievable” (the ALARA safety principle). This is not necessarily the specification set required for successful imaging of higher density objects such as large, heavily permineralized fossils.  
Successful scans of extremely large paleontological objects can, therefore, be challenging. Scanning the skull of one of the largest carnivores ever to have walked the earth is certainly beyond the capabilities of a regular medical CT system. The skull of the remarkably complete T. rex skeleton FMNH PR2081, perhaps better known by its nickname “Sue” (now on display at the Field Museum in Chicago) was scanned -almost two decades agoat Rocketdyne Division of Boeing North America. This scan was completed in a Minatron 205 scanner, yielding 748 coronal slices, 2 mm in thickness (Brochu, 2003). For many paleontological questions however, higher-resolution imaging than 2 mm voxel size is necessary. In this contribution, we elaborate on the technical challenges in scanning the skull of the Naturalis T. rex. A more detailed description of the morphology, partially based on the CT scan data discussed here, will be submitted for publication elsewhere.  3. Results  
The CT reconstruction was performed on the whole dataset including the surrounding crate and support structure. Figure 5 shows one slice through the dataset. Generally, the bones (light grey) can be clearly distinguished from the sandstone matrix (dark grey) due to its significant difference in density. Inside the bone, one can discern occasional high-intensity spots which represent pyrite concretions. Other materials involved in packing and crating have generally much lower X-ray absorption, except for the screws used in the wooden support frame. As can be seen in the upright corner of figure 5 even the polyurethane foam is visible by using a different grey value scaling.  
Figure 6 (left) shows a 3D-rendering of the same dataset. To distinguish the different materials a false-color representation based on the different absorption values of the materials were used. The virtually removed sideways uncovers the wrapping around the skull and sandstone block as well as the additional wooden supporting structures. Figure 6 (right) cuts through the crate in lateral direction and shows the interior of the skull and sandstone block. The white colored structure marks the bone fragments.  
The next step was to virtually excavate the skull. The good material contrast made it possible to mask out the bulk of the sandstone matrix and the supporting structures by setting appropriate thresholds. High absorption parts like the screws as well as noise particles had to be removed manually. The result of this segmentation can be seen in figure 7. At this stage the segmented skull is still represented by three dimensional pixels (Voxels) with a specific absorption value. To allow for further processing in CAD software e.g. for 3D-printing preparation the segmented skull was converted to a triangular surface mesh in the stl Format.  
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 4. Discussion and Outlook   
The scan has already allowed for much more efficient preparation work on the fossil, by showing which areas deserve particular attention. Many internal features are clearly visible, including pneumatic chambers and the portion of the skull that was originally occupied by the brain (Witmer & Ridgely, 2009). Of particular interest are the morphology of the nerve channels, semicircular canals of the inner ear (Witmer & Ridgely, 2009), location and form of the stapes, the possibility of respiratory turbinates (Witmer, 1997; Brochu, 2003; Witmer & Ridgely, 2009), and the fact that this scan shows new fragile structures not visible with lower resolution CT scans - and which we suspect may have been obliterated by mechanical preparation of other specimens. We do hope that this scan, too, will contribute to a more informed reconstruction of soft tissues (Witmer, 1997; Brochu, 2003).  
Part of the magic of X-ray imaging techniques is that the invisible becomes visible. The CT of the T. rex skull allowed for a virtual endocast of the brain cavity to be made (compare Witmer & Ridgely, 2009). A 3D-print of the “brain” of the T. rex (see Figure 8) already played a role in lectures and (online) classes; the printed brain will also find a place in the upcoming exhibition at Naturalis.  
The skull of the new T. rex shows multiple pathologies, some of which are captured in detail in the CT scan. Pathologies include a rather large bone infection which has removed bone tissue in the anterior part of the right maxilla (=the front end of the upper jaw); this element however was discovered separate from the main skull block, and therefore was not part of the scan. The same applies for the posterior mandibular unit (= the rear part of the lower jaw), which is graced by a series of healed puncture wounds; considering the size and spacing of the wounds, in all likelihood this individual was bitten by another T. rex - and lived for the wounds to heal. Other pathologies on the skull include scratch marks on the left side of the skull. At Naturalis we plan to present the CT data of the skull in an interactive display, where a laser line projected on a scaled, moveable 3D-print of the skull acts as a pointer to the CT-imagery shown beside the skull. Interactive “hot zones” allow to connect explanatory text and video to the features highlighted in the scan.
description: Published as part of Reims N, Schulp A, Bohnel M & Larson P, 2016, An XXL-CT-scan of an XXL Tyrannosaurus rex skull, pp. 1-9 in 19 th World Conference on Non-Destructive Testing 2016 on pages 1-8, DOI: 10.5281/zenodo.3479733