Brain Volume Database

ibvd-brain-coloured

The Internet Brain Volume Database (IBVD) is an online collection of neuroimaging data funded as a part of the international initiative, the Human Brain Project. The IBVD provides access data for both individual and among-group comparisons that allow total volume comparisons with parallelization of the brain into hemispheres, specific lobes or grey matter volumes. While the database contains data on humans, there is also non-human primate (macaque) and rat studies. A summary search provides information on sex, age and handedness as well as age-related pathology, neuro-psychiatric disease, structural disease and twin-studies (monozygotic and dizygotic). These selected individuals can be compared to normal studies or pooled into user-specified group results. For example, it is very easy to generate a plot of  left vs. right temporal lobe volume compared to age in normal human in vivo males and females.

Alannah Pearson


Seasonal skull reduction

dechmann-et-al-2017Braincase shrinkage during winter was firstly described in shrews by Dehnel in 1949, and is known as the Dehnel’s Phenomenon. Recently, Dechmann et al. investigated the seasonal size variation in the skulls of shrews (Sorex araneus) and least weasels (Mustela nivalis). They measured skull length and braincase depth on specimens previously collected from a Polish National Park, sampling all seasons. Both species showed an initial juvenile growth until the first winter, followed by shrinkage until spring in the adults, and a subsequent re-grow on the second summer, though never reaching the initial size. Heat maps built from high resolution CT scans demonstrated that size changes also involved changes in shape and in bone thickness, with the thinnest skulls coinciding with the smallest braincase size. Interestingly, these patterns differed between sexes, especially in weasels as only males were observed to re-grow. Despite phylogenetically distant, both species have similar life histories, having short life spans and high metabolisms, and inhabiting an environment with seasonal fluctuation of resources availability. Winter shrinkage would reduce energetic requirements and prepare individuals for the harder conditions, and re-growth during the resources-abundant season would prepare the males for reproduction while females would allocate the energy into caring for the offspring.  The authors conclude these seasonal reversible size changes are genetically fixed and exclusive of animals with such life histories, as an adaptation to extreme environmental conditions. Future investigation shall clarify the potential drivers and consequences of this phenomenon, including how the variation in size affects brain size and reorganization.

Sofia Pedro


FEA, Validity & Sensitivity

fea-validity-smlThe Finite Element Method (FEM) was developed within the framework of Engineering but has become a popular tool in bio-mechanical studies. It is natural that computational bio-mechanics and Finite Element Analysis (FEA) became increasingly promising in fossil studies where there are no examples of some taxa still living. To study the bio-mechanical responses of fossil hominids, modern humans and non-human primates are often used as comparative samples for which there are already known values. Despite this, precisely how accurately computational bio-mechanics compares with physical studies is still not well understood. The biological composition of bone and dentition is hard to replicate in computational terms with the cranium a mixture of trabecular and cortical bone while teeth comprise variable layers of enamel and dentine. The resolution required from Computed Tomography (CT) scans to accurately capture these finer biological compositions is not feasible for the heavy demands on software to analyze such FEA models with flow-effects for the number of specimens that can be included into any single study.

Godinho et al investigated the validity and sensitivity of Finite Element (FE) models using a direct comparison with a human cadaver. Results were particularly affected if the model was simplified by assigning all materials as cortical bone, including dentition and trabecular bone components. Results showed that the real and virtual skull showed no differences in strain magnitude; differences in strain pattern (high or low strain distribution) were only partially different; simplifying the virtual model decreased the strain magnitude; simplifying the virtual model partially affected the strain pattern with the regions near the dentition, particularly the alveolar ridge, most affected.

For bio-mechanical studies, by not simplifying virtual models and attempting to designate dental and bone tissues properly acknowledges the underpinning biology of the cranium while potentially revealing sensitive adaptations of this biological structure. By adopting these changes, new variations between living and fossil humans, that have so-far been obscured by less time-consuming computational methods, could reveal unique adaptational trends that have real significance for human evolution.

Alannah Pearson


Frontal lobes and surface

 

beaudet-and-bruner-2017A surface analysis on the frontal lobes in archaic humans …

[A post]    [The Paper]

 

 


Which One? PLY vs. STL

3d-format As the use of virtual anatomy increases, awareness of different 3D mesh (digital model) formats is useful. Simply, a 3D mesh is the geometrical representation of an anatomical structure such as a cranium, endocast or tooth. Below, are the main differences, benefits, and uses of common PLY and STL 3D formats.

PLY (Stanford Polygon Format) is a 3D file format that was commonly developed from 3D surface scanners and photogrammetry software to allow the preservation of information on surface geometry while retaining information on RGB colour. STL (Stereolithography) is a 3D format commonly generated from software using only grayscale images such as raw CT (Computed Tomography) where RGB colour is not captured. 3D Printers only require preserved information on surface geometry, not colour, leaving STL to be a preferred format for 3D printing technologies.

Even though there is no discernible difference between the quality of the 3D mesh types, PLY format offers binary encoding of all information (including RGB colour). This results in a smaller file size, allowing less space occupied on a hard-drive or cloud-storage and faster loading of the 3D mesh into software programs as employed in 3D-geometric morphometrics.

Alannah Pearson


A frontal sphere

bulut-et-al-2016So far, the majority of new quantitative methods and approaches to investigate sexual dimorphism have focused primarily on the morphology of the five most commonly studied sexually dimorphic traits of the skull (glabella, orbital margins, mastoid process, nuchal crest, and mental eminence), while other cranial traits are still being evaluated in terms of simple subjective descriptions. One of the cranial regions showing great potential for further development of sex estimation techniques is the frontal region. Recently, Bulut and colleagues quantified the shape differences between male and female frontal bones using a novel and landmark-free 3D modeling method. Their new finding that the male frontal bone is actually more spherical than the female is in opposition to the common perception. In their study, CT scans of 80 male and 80 female Caucasian frontal bones from a Turkish population between the age of 25 and 40 years were obtained. The frontal bone was isolated by carrying out the “selection tool” in the GOM Inspect software using STL models. The frontal bone model is aligned to the CAD sphere model, using the best-fit registration method in the GOM Inspect software. Next, the difference in surface morphology between the frontal bone data and the CAD sphere was quantified, using the sphere model as the reference surface. Also, color maps were generated to show the deviations between frontal bone surface and the CAD sphere surface. Deviations of ±1mm were calculated as the overlapping areas. Color maps show that, for males, the areas exhibiting the largest discrepancy between frontal bone and CAD sphere surface are glabella, the supraorbital margins, the zygomatic processes, the superciliary arc, and the temporal face.

The area displaying most overlap with the sphere is the upper frontal region, including the frontal squama and the frontal eminences. For females, the frontal squama showed the main congruence with the sphere surface, while the largest deviations were observed for glabella, the supraorbital margins, the zygomatic processes, the superciliary arch, the frontal eminences, and the temporal face. The amount of frontal bone overlapping with the sphere was found to range from 30.1% to 56.1% for males, and from 19.6% to 48.3% for females. The difference in average values between males (43.2 ± 6.5%) and females (33.9 ± 6.6%) was found to be statistically significant, i.e. p < 0.0001, using the double-sided version of student’s t-test. This finding is in opposition to the common perception that the male frontal bone is more inclined than the female, which is described as more vertical and rounded, convex, smooth, and broad. Using the overlapping surface parameter to develop linear discriminant functions, sex was accurately predicted for 61 of 80 females (76.3%) and 63 of 80 males (78.8%) after leave-one-out cross-validation, yielding an average of 77.5% correct classifications.

Yameng Zhang


Fractal brains

the-fractal-geometry-of-the-brain

[click here!]


Sexual identification

post1Sex assessment is crucial in any survey on human remains.  Musilová et al, have recently published a new method for sexual identification using virtual scans of both male and female individuals. They found that the size of the cranial surface was significantly different between both sexes, being the male skulls larger than the females in some areas, such as the nasal root, external occipital protuberance and mastoids. The most pronounced areas with sexual cranial differences are those linked to muscle attachment, such as supraorbital, frontal and nuchal regions. Sexual dimorphism was significantly lower in senile skulls. This article provides a new and successful method using 3D techniques and geometric morphometrics, interesting for different applications in anthropology.

Gizéh Rangel de Lázaro


Evolution of Nervous Systems II

ens2017

[Elsevier]   [Science Direct]


Mapping the brain

The Rhoton Collection is composed by an outstanding anatomical presentations of the brain created by the renowned surgeon and educator Dr. Albert Rhoton Jr throughout his life. These presentations were made using bright blue and red dyes in the blood vessels, so that surgeons could easily visualize and explore the brain and vascular structures for planning surgical interventions.

[Here a post in Spanish]

Gizéh Rangel de Lázaro