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Review
. 2016 Aug;229(2):173-90.
doi: 10.1111/joa.12378. Epub 2015 Sep 25.

Best practices for digitally constructing endocranial casts: examples from birds and their dinosaurian relatives

Amy M Balanoff  1 , G S Bever  2 , Matthew W Colbert  3 , Julia A Clarke  3 , Daniel J Field  4 , Paul M Gignac  5 , Daniel T Ksepka  6 , Ryan C Ridgely  7 , N Adam Smith  8 , Christopher R Torres  9 , Stig Walsh  10 , Lawrence M Witmer  7
Affiliations
Review

Best practices for digitally constructing endocranial casts: examples from birds and their dinosaurian relatives

Amy M Balanoff et al. J Anat. 2016 Aug.

Abstract

The rapidly expanding interest in, and availability of, digital tomography data to visualize casts of the vertebrate endocranial cavity housing the brain (endocasts) presents new opportunities and challenges to the field of comparative neuroanatomy. The opportunities are many, ranging from the relatively rapid acquisition of data to the unprecedented ability to integrate critically important fossil taxa. The challenges consist of navigating the logistical barriers that often separate a researcher from high-quality data and minimizing the amount of non-biological variation expressed in endocasts - variation that may confound meaningful and synthetic results. Our purpose here is to outline preferred approaches for acquiring digital tomographic data, converting those data to an endocast, and making those endocasts as meaningful as possible when considered in a comparative context. This review is intended to benefit those just getting started in the field but also serves to initiate further discussion between active endocast researchers regarding the best practices for advancing the discipline. Congruent with the theme of this volume, we draw our examples from birds and the highly encephalized non-avian dinosaurs that comprise closely related outgroups along their phylogenetic stem lineage.

Keywords: Aves; brain; comparative neuroanatomy; computed tomography; endocast.

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Figures

Figure 1
Figure 1
Three‐dimensional (3D) renderings of the cranial endocast of Eurypyga helias constructed from CT data. (A) Cranial endocast of E. helias with transparent skull. (B) Cranial endocast of E. helias with cranial nerves (yellow), arteries (red), veins (blue), and inner ear (pink). (C) Cranial endocast of E. helias with inner ear, nerves, and vasculature digitally removed. A smoothing algorithm (Laplacian Smooth) has been applied to the rendering.
Figure 2
Figure 2
CT images and cranial endocasts from different specimen types and preparations. Top row, 3D reconstruction of skull/head from CT data. Second row, representative CT slice through the cranial cavity. Third row, CT slice with the cranial cavity segmented. Fourth row, digitally prepared cranial endocast. (A) A skeletal preparation of the extant galliform bird Alectura lathami. (B) A fossil oviraptorosaur dinosaur, Citipati osmolskae. (C) A contrast‐enhanced iodine‐stained preparation of the extant paleognathous bird Dromaius novaehollandiae. These staining techniques provide a relatively direct bridge between an endocast and the soft tissues it represents, thus expanding the future role of endocasts in comparative neuroscience.
Figure 3
Figure 3
Flow chart illustrating procedures to help determine if high‐resolution CT scanning is the preferred method to deal with the specimen of interest.
Figure 4
Figure 4
Flow chart illustrating preferred procedures for reducing CT data size.
Figure 5
Figure 5
In some cases there is no single threshold value that will correctly select the surface of interest because of partial volume effects. (A) In this example the specimen (Tapirus pinchaque: MVZ 124091) has regions of thin and thick bone. (B). Use of the half‐maximum thresholding protocol will correctly define the surface location in regions of thick bone but not in regions where the bone is too thin to reach the true CT value for bone. (C) Accordingly, the threshold will drop out surfaces defined by thin bone.
Figure 6
Figure 6
Suggested approach for drawing the anatomical cutoff point for openings into the endocranial space such as the foramen magnum. Sagittal slice through skull of Eurypyga helias, in which the endocast has been segmented in the coronal and horizontal planes (blue). The red dotted line indicates where the third line should be drawn to complete this cutoff.
See this image and copyright information in PMC

References

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    1. Balanoff AM, Rowe T (2007) Osteological description of an embryonic skeleton of the extinct elephant bird, Aepyornis (Palaeognathae: Ratitae). J Vertebr Paleontol 27, 1–53.
    1. Balanoff AM, Xu X, Kobayashi Y, et al. (2009) Cranial osteology of the theropod dinosaur Incisivosaurus gauthieri (Theropoda: Oviraptorosauria). Am Mus Novit 3651, 1–35.
    1. Balanoff AM, Bever GS, Ikejiri T (2010) The braincase of Apatosaurus (Dinosauria: Sauropoda) based on computed tomography of a new specimen with comments on variation and evolution in sauropod neuroanatomy. Am Mus Novit 3677, 1–32.

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