Human Atlas Research Articles

37. Use of a dedicated brain phantom in PET/MR

Introduction The attenuation correction of PET/MR brain imaging is based on a human atlas. However, this atlas cannot be used for phantoms employed for the usual PET/CT experiments. The method based on the DIXON MRI is used instead to separate water and fat tissues and assign them attenuation coefficients at 511 keV. Nevertheless, the usual PET/CT phantoms generate artefacts on the MR-based attenuation maps. Additionally, their materials have different attenuation coefficients from those of human body. Here, we suggest to substitute the MR derived attenuation correction map with a CT derived attenuation correction map for a brain phantom in PET/MR. Methods Two PET acquisitions of a 3D Hoffman phantom were achieved: one a PET/CT Biograph mCT Flow (Siemens) and one on a Signa PET/MR (GE). Based on these acquisitions, 4 images were reconstructed: 1 with the PET/CT (PETref) and 3 with the PET/MR (one without attenuation correction (PETNAC), one corrected using MR-based attenuation map (PETMRAC) and one corrected using the CT obtained with the PET/CT, registered on the MRI images (PETCTAC). To evaluate the effect of the different attenuation correction of the PET images, activity concentrations ratio between white matter (WM) and gray matter (GM), as well as between anterior and posterior regions (A/P) and between right and left (R/L) regions, were measured on PETNAC, PETMRACand PETCTAC and compared to the ratios obtained with PETref. Results The MR based attenuation correction map of the Hoffman phantom showed artefacts due to segmentation and tissue classification errors. Moreover, for all the reconstructed images, no R/L asymmetry was observed (ratios between 0.96 and 0.99). However, a strong A/P asymmetry with a mean value of 20% was measured in the PETNAC for both WM and GM, versus 1% for the 3 attenuation-corrected images. The WM/GM ratio was underestimated on the PETMRAC (1.84) compared to the CT-based attenuation-corrected ones (1.95 and 1.96 for PETCTAC and PETref, respectively). Conclusions All the attenuation correction methods allowed to correct the A/P asymmetry, which was increased by the presence of MR coil in the PET/MR system. However, MR-based attenuation-correction map suffered from artefacts and was not adapted to correct the PET image of the Hoffman phantom in PET/MR. The CT-based attenuation correction method used to correct the Hoffman phantom PET/MR image showed ratios comparable to the ones measured on a PET/CT considered as reference.

376 Human Connectome-Based Tractographic Atlas of the Brainstem Connections and Surgical Approaches

Abstract INTRODUCTION The brainstem is one of the most challenging areas for the neuro- surgeon because of the limited space between gray matter nuclei and white matter pathways. Diffusion tensor imaging based tractography has been used to study the brainstem structure, but the angular and spatial resolution could be improved further with advanced diffusion magnetic resonance imaging (MRI). Objective: To construct a high angular/spatial resolution, wide-population based, comprehensive tractography atlas that presents an anatomical review of the surgical approaches to the brainstem. METHODS We applied advanced diffusion MRI finer tractography to a population-based atlas constructed with data from a total of 488 subjects from the Human Connectome Project-488. Five formalin-fixed brains were studied for surgical landmarks. Luxol Fast Blue stained histological sections were used to validate the results of tractography. RESULTS >We acquired the tractography of the major brainstem pathways and vali- dated them with histological analysis. The pathways included the cerebellar peduncles, corticospinal tract, corticopontine tracts, medial lemniscus, lateral lemniscus, spino- thalamic tract, rubrospinal tract, central tegmental tract, medial longitudinal fasciculus, and dorsal longitudinal fasciculus. Then, the reconstructed 3-dimensional brainstem structure was sectioned at the level of classic surgical approaches, namely supra- collicular, infracollicular, lateral mesencephalic, perioculomotor, peritrigeminal, antero- lateral (to the medulla), and retro-olivary approaches. CONCLUSION The advanced diffusion MRI fiber tracking is a powerful tool to explore the brainstem neuroanatomy and to achieve a better understanding of surgical approaches.

Sexing Adult Human Atlas Vertebrae in South India

Sexing Adult Human Atlas Vertebrae in South India

Creation of a paediatric head voxel model database for dosimetric applications

Introduction CBCT is a recently introduced imaging modality in dentomaxillofacial radiology with increasing applications to paediatric cohorts. To accurately estimate the radiation induced risk via Monte Carlo (MC) simulations, age and gender specific head and neck voxel models should be built. These models will enable organ dose calculations and accurate risk estimation via effective dose (ED) or Life Attributable risk (LAR). Purpose To design a head and neck voxel model database for MC dosimetry. Methods and materials Our voxel models were based on organ segmentation of CT image datasets with following characteristics: represent a complete head; have a good low contrast resolution (as the many soft tissues are close in density), have the thyroid included in the scan. Using our PACS database, 13 datasets of paediatric patients from 5 to 14 years old were found to meet the requirements for further processing. From each CT scan, 22 organs were manually segmented on an organ by organ using ImageJ, Matlab tools and human atlases (example: http://headneckbrainspine.com/Neck-CT.php ). Organ masses were compared to ICRP reference values. Results 13 paediatric voxel phantoms were created and compared favourably with ICRP values: 7 males and 6 females. The in-plane resolution of the phantoms, determined by the axial voxel size dimensions, ranges from 0.21 × 0.21 mm 2 to 0.48 × 0.48 mm 2 ; the z resolution ranges from 0.6 mm to 3.22 mm. Conclusion The database for paediatric CBCT applications can now be used for detailed dose and risk applications.

Development and Implementation of a Corriedale Ovine Brain Atlas for Use in Atlas-Based Segmentation.

Segmentation is the process of partitioning an image into subdivisions and can be applied to medical images to isolate anatomical or pathological areas for further analysis. This process can be done manually or automated by the use of image processing computer packages. Atlas-based segmentation automates this process by the use of a pre-labelled template and a registration algorithm. We developed an ovine brain atlas that can be used as a model for neurological conditions such as Parkinson’s disease and focal epilepsy. 17 female Corriedale ovine brains were imaged in-vivo in a 1.5T (low-resolution) MRI scanner. 13 of the low-resolution images were combined using a template construction algorithm to form a low-resolution template. The template was labelled to form an atlas and tested by comparing manual with atlas-based segmentations against the remaining four low-resolution images. The comparisons were in the form of similarity metrics used in previous segmentation research. Dice Similarity Coefficients were utilised to determine the degree of overlap between eight independent, manual and atlas-based segmentations, with values ranging from 0 (no overlap) to 1 (complete overlap). For 7 of these 8 segmented areas, we achieved a Dice Similarity Coefficient of 0.5–0.8. The amygdala was difficult to segment due to its variable location and similar intensity to surrounding tissues resulting in Dice Coefficients of 0.0–0.2. We developed a low resolution ovine brain atlas with eight clinically relevant areas labelled. This brain atlas performed comparably to prior human atlases described in the literature and to intra-observer error providing an atlas that can be used to guide further research using ovine brains as a model and is hosted online for public access.

English

English

Morphometric analyses of atlas vertebrae-A cross sectional study

Introduction: Knowledge about morphometric measurements related to atlas vertebra are important for neurologists, neurosurgeons and head and neck surgeons who deal with traumatic or non-traumatic conditions which may lead to altanto-axial and atlanto- occipital instability. The aim of the present study was to assess the various parameters on the atlas vertebra which can help to determine the safe sites for the different surgical approaches. Materials and Methods: Study was carried out on 50 dry south Indian adult human atlas vertebrae of unknown sex which were collected from the department of anatomy. Eleven parameters were measured for each atlas using a digital vernier caliper. Results: Range, mean and standard deviations were measured and recorded and bilateral symmetry was observed. Conclusion: The parameters measured in the present study may help surgeons in avoiding and reducing complications such as vertebral artery injury, spinal cord injury during the surgical corrections of atlanto axial or atlanto occipital instability. Keywords: Atlas, vertebrae, Atlanto-axial, Atlanto-occipital, Interlaminar clamps

Morphometric Analysis of Atlas and Its Clinical Significance: An Anatomical Study of Indian Human Atlas Vertebrae

The morphometry of atlas is very important for surgeries in the occipitocervical region. There are studies explicitly differing in the results concerning some key anatomic measurements, mandating an additional evaluation of anatomic landmarks of atlas. Therefore, this study was aimed to evaluate the various dimensions of the atlas quantitatively relevant for various surgeries. A total of 30 adult atlas vertebrae of Indian origin were studied. The distances were measured by digital vernier calliper. The transverse diameter and maximum anteroposterior dimension of vertebral canal of atlas had a mean of 27.31 ± 2.74 and 29.44 ± 2.54 mm, respectively. The vertebral artery groove thickness on atlas is 3.79 ± 1.08 mm on right and 4.05 ± 00.86 mm on left, respectively. The mean distance from sagittal midline to the innermost edge of the vertebral artery groove is 10.73 ± 2.92 mm on right side and 09.72 ± 2.56 mm on left side. Overall, 74% of superior articular facets were found to be oval in shape and 26% in kidney shape. On the basis of these findings, we concluded that the thickness of the vertebral artery groove is satisfactory for surgical fixation techniques and the dissection on the posterior arch of atlas can be extended to 12 mm from the midline through the posterior approach.

Incidence of Ponticles in Human Atlas Vertebrae-A Study from South Gujarat Population

Background: Atlas, an atypical 1st cervical vertebra bears anterior and posterior arch. The superior surface of posterior arch presents groove for vertebral artery. Sometimes bony out growth extending from superior articular process to the posterior arch is known as ponticle which may cause external pressure on the vertebral artery when latter passes from foramen transversarium to foramen magnum of the skull. Aim: The study was to find out an incidence of atlas ponticles (bridges) for its clinical and surgical significance. Materials and Methods: In this study, 50 dried macerated atlas vertebrae of unknown age and sex were collected from department of anatomy of medical colleges of South Gujarat and examined for presence of ponticles. Results: Out of 50 atlas vertebrae, total 11 (22%) bones presented with ponticles of which incidence of posterior ponticle was seen in 10 (20%) cases and lateral ponticle in 1 (2%) case. Total incidence of complete and incomplete variety was noted in 5 (10%) and 6 (12%) cases respectively. Incidence of bilateral ponticle was observed in 2 (4%) while unilateral in 9 (18%) vertebrae of which 5 (10%) right sided and 4 (8%) left sided. Conclusion: The presence of ponticles may reduce the cross sectional area of vertebral artery, compromising its blood flow resulting in vertebro-basilar insufficiency which may lead to various types of neurological symptoms like dizziness, fainting, transient diplopia and vertigo. Key Words: Atlas vertebra, Ponticle, Vertebral artery groove

Length and Thickness of Vertebral Artery Groove of Dry Ossified Human Atlas Vertebra

Context: The superior surface of the posterior arch of the atlas vertebra behind its lateral mass has a vertebral artery groove. The contents of this groove are third part of vertebral artery, venous plexus and first cervical nerve. Morphometric data of vertebral artery groove is helpful for the spine surgeons to avoid iatrogenic injury of these vital structures during posterior approach.
 Materials and Methods: A cross-sectional, analytical type of study was conducted in the Department of Anatomy, Dhaka Medical College, Dhaka from January 2012 to July 2013. Inner and outer groove length and thickness of the vertebral artery groove was measured with the help of flexible metallic wire and digital slide calipers.
 Results: There was no significant difference (P>0.10) in the mean length of inner border between right and left groove for vertebral artery. But outer border of left groove for vertebral artery was larger than right groove for vertebral artery (P<0.001). The mean thickness of the groove for the right and left vertebral artery was not significantly different (P>0.50).
 Bangladesh J. Anat. 2015; 13(1) : 8-10

Book Review: Comparative Anatomy and Histology: A Mouse and Human Atlas

Book Review: Comparative Anatomy and Histology: A Mouse and Human Atlas

Human Atlas of the Cardiac Fiber Architecture: Study on a Healthy Population

Cardiac fibers, as well as their local arrangement in laminar sheets, have a complex spatial variation of their orientation that has an important role in mechanical and electrical cardiac functions. In this paper, a statistical atlas of this cardiac fiber architecture is built for the first time using human datasets. This atlas provides an average description of the human cardiac fiber architecture along with its variability within the population. In this study, the population is composed of ten healthy human hearts whose cardiac fiber architecture is imaged ex vivo with DT-MRI acquisitions. The atlas construction is based on a computational framework that minimizes user interactions and combines most recent advances in image analysis: graph cuts for segmentation, symmetric log-domain diffeomorphic demons for registration, and log-Euclidean metric for diffusion tensor processing and statistical analysis. Results show that the helix angle of the average fiber orientation is highly correlated to the transmural depth and ranges from -41° on the epicardium to +66° on the endocardium. Moreover, we find that the fiber orientation dispersion across the population (±13°) is lower than for the laminar sheets (±31°) . This study, based on human hearts, extends previous studies on other mammals with concurring conclusions and provides a description of the cardiac fiber architecture more specific to human and better suited for clinical applications. Indeed, this statistical atlas can help to improve the computational models used for radio-frequency ablation, cardiac resynchronization therapy, surgical ventricular restoration, or diagnosis and followups of heart diseases due to fiber architecture anomalies.

Translational Proteomics in Neurodegenerative Diseases - 16th HUPO BPP Workshop September 5, 2011, Geneva, Switzerland

The HUPO Brain Proteome Project (HUPO BPP) held its 16th workshop in Geneva, Switzerland, on September 5, 2011 during the 10th HUPO World Congress. The focus was on launching the Human Brain Proteome Atlas as well as ideas, strategies and methodological aspects in clinical neuroproteomics.

Creating a human brain proteome atlas - 14th HUPO BPP workshop September 20-21, 2010, Sydney, Australia

The HUPO Brain Proteome Project (HUPO BPP) held its 14th workshop during the HUPO 9th Annual World Congress in Sydney, Australia. The principal aim of this project is to discover prognostic and diagnostic biomarkers associated with neurodegenerative diseases and brain aging, with the ultimate objective of obtaining a better understanding of these conditions and creating roads for the development of novel diagnostic techniques and effective treatments. The attendees came together to discuss progress in the human clinical neuroproteomics and to define the needs and guidelines required for more advanced proteomics approaches.

Mapping the brain: of mice and men

“When we set out to develop the Allen Mouse Brain Atlas some 8 years ago, there were those who said it couldn’t be done”, recalls Allan Jones, chief executive offi cer of the Allen Institute for Brain Science in Seattle (WA, USA). Those doubters were proved emphatically wrong in 2006, when the Institute published the fi rst genomically and anatomically complete map of the mouse brain, allowing users of the free resource to pinpoint the expression of genes in the mouse brain at the level of individual cells. The atlas has already notched up more than 500 citations in peerreviewed studies. But for Jones, the mouse brain was just a warm-up. “Model systems are fantastic tools for modern science, but we ultimately want to understand the human brain in its normal and disease context, and a comprehensive human brain dataset certainly helps”, Jones told The Lancet Neurology, after the Institute launched its latest application: the Allen Human Brain Atlas. Like the mouse brain atlas, the human brain atlas is free to access, and was designed from the outset with researchers in mind. “It displays the gene-expression map for any gene in the human brain in an interactive platform so the user can spin, splice, or manipulate the image in just about any way...and then navigate directly to the detailed, raw data underlying the 3D summary views”, explains Jones. And if you still want more, there are a host of other tools to investigate the data online, along with all the original images, gene-expression data, and MRI data to download.

ChemInform Abstract: Human Protein Atlas of Redox Systems — What Can Be Learnt?

AbstractReview: 89 refs.

Posterior arch defect in a dry atlas

The human atlas can be divided anatomically into three parts: the anterior arch, the lateral masses, and the posterior arch.

Evaluation of anatomic landmarks and safe zones for screw placement in the atlas via the posterior arch

Several studies have evaluated quantitative anatomic data for direct lateral mass screw fixation. To analyze anatomic landmarks and safe zones for optimal screw placement through the posterior arc of the human atlas, morphometric parameters of 41 adult native human atlas specimens were quantitatively measured. Internal dimensions of the atlas (lateral mass, maximum and minimum intraosseous screw length), minimum height and width of the posterior arc and optimal screw insertion angles were defined on pQCT scans. By this, an optimal posterior screw insertion point (OIP) and a preferable screw direction (PSD) through the posterior arch into the lateral mass of C1 were defined. External dimensions (transverse and sagittal diameter) as well as the width of the mid-portion of C1 lateral mass were significantly higher in male specimens. The mean height of the posterior arch at the vertebral artery groove was 4.1 +/- 0.8 mm in female and 4.6 +/- 0.9 mm in male specimens. The optimal screw insertion point was located 21.6 +/- 1.7 mm in female and 23.6 +/- 2.3 mm in male lateral from the posterior tubercle of C1 (P < 0.01). The preferable screw direction was a mean medial inclination of 7.9 +/- 1.9 degrees in female and 7.3 +/- 2.7 degrees in male specimens and a mean rostral direction of 2.4 +/- 1.8 degrees in female and 3.1 +/- 1.7 degrees in male specimens. In conclusion, the presented study provides information for the use and design of upper cervical spine instrumentation techniques, such as screw placement to C1 via the posterior arch. The characterization of working areas and safe zones (OIP, PSD) might contribute to a minimization of screw malposition in this highly demanding instrumentation technique.

Transverse Foramen of the Atlas (C1) Anteriorly Unclosed

Morphologic study of 500 human adult atlases, 256 atlases of nonhuman adult primates representing 37 genera, and 25 human atlases of newborns and young individuals from birth to 3 years of age. To provide original observations to attempt to understand the anterior unclosure of the transverse foramen of the human atlas, to ascertain its occurrence in primates, and to offer some elements regarding the evolutionary and functional significance of this disposition. Anteriorly unclosed transverse foramen is one of the classic variants of the human atlas, however, rare quantitative data are available in the literature and this disposition remains little understood. Macroscopical study (dried bones). In humans, an anteriorly unclosed transverse foramen was observed on one or both sides in 51 individuals of the 500 in the present series (10.2%); bilateral occurrence (symmetric manifestation) was observed in 45.1% of the anterior unclosures and unilateral occurrence in 54.9%; no significant right or left predominance was observed in the frequency of lateral occurrence. In human newborns and young individuals (from birth to 3 years of age), the transverse foramen was anteriorly unclosed in all of the 25 cases studied. In nonhuman primates, some bilateral or unilateral cases of anterior unclosure were only observed in hominoids, except gibbons: orangutans (8.3%), gorillas (10.5%), and chimpanzees (14.3%). The anteriorly unclosed transverse foramen of the atlas seems to be the result of an evolutionary tendency characteristic of hominoids within primates and could be interpreted as a shared derived character (i.e., synapomorphy) and as the persistence in adults of a juvenile pattern (i.e., paedomorphosis). It must not be interpreted as a pathologic erosion or destruction but as being a simple normal variant.

Human Atlas Projects from RNA to Proteins

Human Atlas Projects from RNA to Proteins