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1.  Body-Painting: A Tool Which Can Be Used to Teach Surface Anatomy 
Introduction
The primary method of learning the surface anatomy is by making the students mark structures on mummified bodies. The students feel that learning the surface anatomy on mummified cadavers is not interesting. The present project on learning the surface anatomy through the body painting method was undertaken to evoke interest among the students.
Materials and Methods
Physiotherapy and dental undergraduate students who volunteered were involved in this study. A few surface anatomy classes were conducted by using the traditional method and a few more by using the body painting exercise. Non toxic body paints of various colours and brushes of different sizes were used for the body painting.
Results
A feedback was obtained from the students by using a structured questionnaire. The students opined that the body painting method was advantageous to them in learning the human anatomy. They also felt that they could have more practice sessions in any setting other than in the classroom and that they did not need to rely upon the mummified bodies. They described the body painting method as self explanatory, which gave them the feel of live structures.
Conclusion
This project was successful in achieving its objectives as the students felt that the method was exciting, with lots of fun during the learning. The body painting method was well accepted by the students as an effective method for learning the surface and the clinical anatomy.
doi:10.7860/JCDR/2012/4700.2370
PMCID: PMC3471490  PMID: 23205358
Living anatomy; Body painting; Medical education; Visual images; Memory
2.  Variability of the temporal bone surface's topography: implications for otologic surgery 
Proceedings of SPIE  2012;8316:83161B-.
Otologic surgery is performed for a variety of reasons including treatment of recurrent ear infections, alleviation of dizziness, and restoration of hearing loss. A typical ear surgery consists of a tympanomastoidectomy in which both the middle ear is explored via a tympanic membrane flap and the bone behind the ear is removed via mastoidectomy to treat disease and/or provide additional access. The mastoid dissection is performed using a high-speed drill to excavate bone based on a pre-operative CT scan. Intraoperatively, the surface of the mastoid component of the temporal bone provides visual feedback allowing the surgeon to guide their dissection. Dissection begins in “safe areas” which, based on surface topography, are believed to be correlated with greatest distance from surface to vital anatomy thus decreasing the chance of injury to the brain, large blood vessels (e.g. the internal jugular vein and internal carotid artery), the inner ear, and the facial nerve. “Safe areas” have been identified based on surgical experience with no identifiable studies showing correlation of the surface with subsurface anatomy. The purpose of our study was to investigate whether such a correlation exists. Through a three-step registration process, we defined a correspondence between each of twenty five clinically-applicable temporal bone CT scans of patients and an atlas and explored displacement and angular differences of surface topography and depth of critical structures from the surface of the skull. The results of this study reflect current knowledge of osteogenesis and anatomy. Based on two features (distance and angular difference), two regions (suprahelical and posterior) of the temporal bone show the least variability between surface and subsurface anatomy.
doi:10.1117/12.911373
PMCID: PMC3766961  PMID: 24027621
temporal bone; bone topography; otologic surgery; robotic surgery; universal stereotactic frame
3.  Computed tomography model-based treatment of atrial fibrillation and atrial macro-re-entrant tachycardia 
Europace  2008;10(8):939-948.
Aims
Accurate orientation within true three-dimensional (3D) anatomies is essential for the successful radiofrequency (RF) catheter ablation of atrial fibrillation (AF) and atrial macro-re-entrant tachycardia (MRT). In this prospective study, ablation of AF and MRT was performed exclusively using a pre-acquired and integrated computed tomography (CT) image for anatomical 3D orientation without electro-anatomic reconstruction of the left atrium (LA).
Methods and results
Fifty-four consecutive patients suffering from AF (n = 36) and/or MRT (n = 18) underwent RF catheter ablation. A 3D CT image was registered into the NavX-Ensite system without reconstruction of the atrial chamber anatomy. The quality of CT alignment was assessed and validated according to fluoroscopy information, electrogram characteristics, and tactile feedback at 31 pre-defined LA control points. The ablation of AF as well as mapping and ablation of MRT was performed within the 3D CT anatomy. In all patients, mapping and ablation could be performed without the reconstruction of the respective atrial chamber anatomy. The overall CT alignment was highly accurate with true surface contact in 90% (84%; 100%) of the control points. Complete isolation of all pulmonary vein (PV) funnels was achieved in 35 of 36 patients (97%) with AF. In patients with persistent AF (n = 11), additional isolation of the posterior LA (box lesion) and the placement of a mitral isthmus line were performed. The MRT mechanisms were as follows: around a PV ostium (n = 6), perimitral (n = 4), through LA roof (n = 5), septal (n = 2), and around left atrial appendage (n = 1). After a follow-up of 122 ± 33 days, 22/25 (88%) patients with paroxysmal AF, 8/11 (73%) with persistent AF, and 16/18 (89%) with MRT remained free from arrhythmia recurrences.
Conclusion
For patients with AF and MRT, our study shows the feasibility of successful placement of complex linear ablation line concepts guided by an integrated 3D image anatomy alone rather than catheter-based virtual chamber surface reconstructions.
doi:10.1093/europace/eun147
PMCID: PMC2488147  PMID: 18577508
Atrial fibrillation; Ablation; Three dimensional image; Model-guided therapy
4.  Analysis of inter-subject variations in intracochlear and middle ear surface anatomy for cochlear implantation 
Hypothesis
We hypothesize that surface landmarks surrounding the round window typically used to guide electrode placement during cochlear implantation (CI) exhibit substantial variability with respect to intracochlear anatomy.
Background
Recent publications suggest that both atraumatic electrode insertion and electrode location within the scala tympani can affect auditory performance after CI. However, current techniques for electrode insertion rely on surface landmarks alone for navigation, without actual visualization of intracochlear structures other than what can be seen through a surgically-created cochleostomy. In this study we quantify how well the position of intracochlear anatomy is predicted by surface landmarks surrounding the round window.
Methods
Structures representing middle ear surface and intracochlear anatomy were reconstructed in μCT scans of 10 temporal bone specimens. These structures were then re-oriented into a normalized coordinate system to facilitate measurement of inter-subject anatomical shape variations.
Results
Only minor inter-subject variations were detected for intracochlear anatomy (maximum deviation = 0.71 mm, standard deviation = 0.21 mm), with greatest differences existing near the hook and apex. Larger inter-subject variations in intracochlear structures were detected when considered relative to surface landmarks surrounding the round window (maximum deviation = 0.83 mm, standard deviation = 0.54 mm).
Conclusions
The cochlea and its scala exhibit considerable variability in relation to middle ear surface landmarks. While support for more precise, atraumatic CI electrode insertion techniques is growing in the otologic community, landmark guided insertion techniques have limited precision. Refining the CI insertion process may require the development of image-guidance systems for use in otologic surgery.
doi:10.1097/MAO.0b013e3182a1a7e6
PMCID: PMC3831172  PMID: 24232065
5.  Mapping cortical anatomy in preschool aged children with autism using surface-based morphometry☆ 
NeuroImage : Clinical  2012;2:111-119.
The challenges of gathering in-vivo measures of brain anatomy from young children have limited the number of independent studies examining neuroanatomical differences between children with autism and typically developing controls (TDCs) during early life, and almost all studies in this critical developmental window focus on global or lobar measures of brain volume. Using a novel cohort of young males with Autistic Disorder and TDCs aged 2 to 5 years, we (i) tested for group differences in traditional measures of global anatomy (total brain, total white, total gray and total cortical volume), and (ii) employed surface-based methods for cortical morphometry to directly measure the two biologically distinct sub-components of cortical volume (CV) at high spatial resolution—cortical thickness (CT) and surface area (SA). While measures of global brain anatomy did not show statistically significant group differences, children with autism showed focal, and CT-specific anatomical disruptions compared to TDCs, consisting of relative cortical thickening in regions with central roles in behavioral regulation, and the processing of language, biological movement and social information. Our findings demonstrate the focal nature of brain involvement in early autism, and provide more spatially and morphometrically specific anatomical phenotypes for subsequent translational study.
Highlights
► First surface-based mapping of cortical anatomy in preschoolers with autism ► Cortical abnormalities at early ages in autism are focal rather than global. ► Early abnormalities already target social cognition and executive control systems. ► All significant abnormalities involve cortical thickness rather than surface area.
doi:10.1016/j.nicl.2012.10.005
PMCID: PMC3777762  PMID: 24179764
Cortical thickness; Surface area; Autism; Neuroimaging
6.  Shaping Skeletal Growth by Modular Regulatory Elements in the Bmp5 Gene 
PLoS Genetics  2008;4(12):e1000308.
Cartilage and bone are formed into a remarkable range of shapes and sizes that underlie many anatomical adaptations to different lifestyles in vertebrates. Although the morphological blueprints for individual cartilage and bony structures must somehow be encoded in the genome, we currently know little about the detailed genomic mechanisms that direct precise growth patterns for particular bones. We have carried out large-scale enhancer surveys to identify the regulatory architecture controlling developmental expression of the mouse Bmp5 gene, which encodes a secreted signaling molecule required for normal morphology of specific skeletal features. Although Bmp5 is expressed in many skeletal precursors, different enhancers control expression in individual bones. Remarkably, we show here that different enhancers also exist for highly restricted spatial subdomains along the surface of individual skeletal structures, including ribs and nasal cartilages. Transgenic, null, and regulatory mutations confirm that these anatomy-specific sequences are sufficient to trigger local changes in skeletal morphology and are required for establishing normal growth rates on separate bone surfaces. Our findings suggest that individual bones are composite structures whose detailed growth patterns are built from many smaller lineage and gene expression domains. Individual enhancers in BMP genes provide a genomic mechanism for controlling precise growth domains in particular cartilages and bones, making it possible to separately regulate skeletal anatomy at highly specific locations in the body.
Author Summary
Every bone in the skeleton has a specific shape and size. These characteristic features must be under separate genetic control, because individual bones can undergo striking morphological changes in different species. Researchers have long postulated that the morphology of individual bones arises from the local activity of many separate growth domains around each bone's surface. Differential growth within such domains could modify size, curvature, and formation of specific processes. Here, we show that local growth domains around individual bones are controlled by independent regulatory sequences in bone morphogenetic protein (BMP) genes. We identify multiple regulatory sequences in the Bmp5 gene that control expression in particular bones, rather than all bones. We show that some of these elements are remarkably specific for individual subdomains around the surface of individual bones. Finally, we show that local BMP signaling is necessary and sufficient to trigger highly localized growth patterns in ribs and nasal cartilages. These results suggest that the detailed pattern of growth of individual skeletal structures is encoded in part by multiple regulatory sequences in BMP genes. Gain and loss of anatomy-specific sequences in BMP genes may provide a flexible genomic mechanism for modifying local skeletal anatomy during vertebrate evolution.
doi:10.1371/journal.pgen.1000308
PMCID: PMC2592695  PMID: 19096511
7.  Correction of Distortion in Flattened Representations of the Cortical Surface Allows Prediction of V1-V3 Functional Organization from Anatomy 
PLoS Computational Biology  2014;10(3):e1003538.
Several domains of neuroscience offer map-like models that link location on the cortical surface to properties of sensory representation. Within cortical visual areas V1, V2, and V3, algebraic transformations can relate position in the visual field to the retinotopic representation on the flattened cortical sheet. A limit to the practical application of this structure-function model is that the cortex, while topologically a two-dimensional surface, is curved. Flattening of the curved surface to a plane unavoidably introduces local geometric distortions that are not accounted for in idealized models. Here, we show that this limitation is overcome by correcting the geometric distortion induced by cortical flattening. We use a mass-spring-damper simulation to create a registration between functional MRI retinotopic mapping data of visual areas V1, V2, and V3 and an algebraic model of retinotopy. This registration is then applied to the flattened cortical surface anatomy to create an anatomical template that is linked to the algebraic retinotopic model. This registered cortical template can be used to accurately predict the location and retinotopic organization of these early visual areas from cortical anatomy alone. Moreover, we show that prediction accuracy remains when extrapolating beyond the range of data used to inform the model, indicating that the registration reflects the retinotopic organization of visual cortex. We provide code for the mass-spring-damper technique, which has general utility for the registration of cortical structure and function beyond the visual cortex.
Author Summary
A two-dimensional projection of the visual world, termed a retinotopic map, is spread across the striate and extra-striate areas of the human brain. The organization of retinotopic maps has been described with algebraic functions that map position in the visual field to points on the cortical surface. These functions represent the cortical surface as a flat sheet. In fact, the surface of the brain is intrinsically curved. Flattening the cortical surface thus introduces geometric distortions of the cortical sheet that limit the fitting of algebraic functions to actual brain imaging data. We present a technique to fix the problem of geometric distortions. We collected retinotopic mapping data using functional MRI from a group of people. We treated the cortical surface as a mass-spring-damper system and corrected the topology of the cortical surface to register the functional imaging data to an algebraic model of retinotopic organization. From this registration we construct a template that is able to predict the retinotopic organization of cortical visual areas V1, V2, and V3 using only the brain anatomy of a subject. The accuracy of this prediction is comparable to that of functional measurement itself.
doi:10.1371/journal.pcbi.1003538
PMCID: PMC3967932  PMID: 24676149
8.  DigiWarp: a method for deformable mouse atlas warping to surface topographic data 
Physics in medicine and biology  2010;55(20):6197-6214.
For pre-clinical bioluminescence or fluorescence optical tomography, the animal's surface topography and internal anatomy need to be estimated for improving the quantitative accuracy of reconstructed images. The animal's surface profile can be measured by all-optical systems, but estimation of the internal anatomy using optical techniques is non-trivial. A 3D anatomical mouse atlas may be warped to the estimated surface. However, fitting an atlas to surface topography data is challenging because of variations in the posture and morphology of imaged mice. In addition, acquisition of partial data (for example, from limited views or with limited sampling) can make the warping problem ill-conditioned. Here, we present a method for fitting a deformable mouse atlas to surface topographic range data acquired by an optical system. As an initialization procedure, we match the posture of the atlas to the posture of the mouse being imaged using landmark constraints. The asymmetric L2 pseudo-distance between the atlas surface and the mouse surface is then minimized in order to register two data sets. A Laplacian prior is used to ensure smoothness of the surface warping field. Once the atlas surface is normalized to match the range data, the internal anatomy is transformed using elastic energy minimization. We present results from performance evaluation studies of our method where we have measured the volumetric overlap between the internal organs delineated directly from MRI or CT and those estimated by our proposed warping scheme. Computed Dice coefficients indicate excellent overlap in the brain and the heart, with fair agreement in the kidneys and the bladder.
doi:10.1088/0031-9155/55/20/011
PMCID: PMC3051844  PMID: 20885019
9.  Complexity of the thoracic spine pedicle anatomy 
European Spine Journal  1997;6(1):19-24.
Transpedicular screw fixation provides rigid stabilization of the thoracolumbar spine. For accurate insertion of screws into the pedicles and to avoid pedicle cortex perforations, more precise knowledge of the anatomy of the pedicles is necessary. This study was designed to visualize graphically the surface anatomy and internal architecture of the pedicles of the thoracic spine. Fifteen vertebrae distributed equally among the upper, middle, and lower thoracic regions were used. For the purpose of mapping surface anatomy, each pedicle was cleaned, spraypainted white, and marked with more than 100 fine points. Using an optoelectronic digitizer, three-dimensional coordinates of the marked points and three additonal points, representing a coordiate system, were digitized. A solid modeling computer program was used to create three-dimensional surface images of the pedicle. To obtain cross-sectional information, each pedicle was sectioned with a thin diamond-blade saw to obtain four slices, 1 mm in thcikness and 0.5 mm apart. The pedicle slices were X-rayed and projected onto a digitizer. The internal and external contours were digitized and converted into graphs by a computer. The pedicles exhibited significant variability in their shape and orientation, not only from region to region within the thoracic spine, but also within the same region and even within the same pedicle. These variations are extremely significant in light of current techniques utilized in transpedicular screw fixation in the thoracic spine. Information documenting the three-dimensional complexity of pedicle anatomy should be valuable for surgeons and investigators interested in spinal instrumentation.
doi:10.1007/BF01676570
PMCID: PMC3454633  PMID: 9093823
Anatomy; Pedicles; Thoracic spine; Pedicle instrumentation; Biomechanics
10.  Hybrid Computational Phantoms Representing the Reference Adult Male and Adult Female: Construction and Applications for Retrospective Dosimetry 
Health physics  2012;102(3):10.1097/HP.0b013e318235163f.
Currently, two classes of the computational phantoms have been developed for dosimetry calculation: (1) stylized (or mathematical) and (2) voxel (or tomographic) phantoms describing human anatomy through mathematical surface equations and 3D voxel matrices, respectively. Mathematical surface equations in stylized phantoms are flexible but the resulting anatomy is not as realistic. Voxel phantoms display far better anatomical realism, but they are limited in terms of their ability to alter organ shape, position, and depth, as well as body posture. A new class of computational phantoms - called hybrid phantoms - takes advantage of the best features of stylized and voxel phantoms - flexibility and anatomical realism, respectively. In the current study, hybrid computational phantoms representing the adult male and female reference anatomy and anthropometry are presented. These phantoms serve as the starting framework for creating patient or worker sculpted whole-body phantoms for retrospective dose reconstruction. Contours of major organs and tissues were converted or segmented from computed tomography images of a 36-year Korean volunteer and a 25-year U.S. female patient, respectively, with supplemental high-resolution CT images for the cranium. Polygon mesh models for the major organs and tissues were reconstructed and imported into Rhinoceros™ for non-uniform rational B-spline (NURBS) surface modeling. The resulting NURBS/polygon mesh models representing body contour and internal anatomy were matched to anthropometric data and reference organ mass data provided by Centers for Disease Control and Prevention (CDC) and International Commission on Radiation Protection (ICRP), respectively. Finally, two hybrid adult male and female phantoms were completed where a total of 8 anthropometric data categories were matched to standard values within 4% and organ volumes matched to ICRP data within 1% with the exception of total skin. The hybrid phantoms were voxelized from the NURBS phantoms at resolutions of 0.158 × 0.158 × 0.158 cm3 and 0.126 × 0.126 × 0.126 cm3 for the male and female, respectively. To highlight the flexibility of the hybrid phantoms, graphical displays are given of (1) underweight and overweight adult male phantoms, (2) a sitting position for the adult female phantom, and (3) extraction and higher-resolution voxelization of the small intestine for localized dosimetry of mucosal and stem cell layers. These phantoms are used to model radioactively contaminated individuals and to then assess time-dependent detector count rate thresholds corresponding to 50, 250, and 500 mSv effective dose, as might be needed during in-field radiological triage by first responders or first receivers.
doi:10.1097/HP.0b013e318235163f
PMCID: PMC3859249  PMID: 22315022
Hybrid phantoms; internal dosimetry; dose assessment; retrospective dosimetry
11.  Anatomy of the abdomen, back, and pelvis as displayed by magnetic resonance imaging: Part One. 
In April 1986, magnetic resonance imaging (MRI) of the thorax and shoulder girdle was presented to the 99th Annual Meeting of the American Association of Anatomists. These images were the authors' first attempt to correlate the magnetic resonance display of the muscles and soft tissues of the chest in the coronal plane with surface gross anatomy. The original purpose of this study was to introduce the role of magnetic resonance imaging to anatomists, medical students, and the specialty of radiology. However, this approach has been expanded by imaging other sections of the body and applying the display of surface anatomy to augment the teaching of anatomy to surgical oncology, pathology, and kinesiology. This three-part article will display magnetic resonance images and will explain how magnetic imaging of the soft tissues can visually augment the teaching of gross anatomy without dissecting surface tissues.
Images
PMCID: PMC2625813  PMID: 2746690
12.  Anatomy of the abdomen, back, and pelvis as displayed by magnetic resonance imaging: Part Two. 
In April 1986, magnetic resonance imaging (MRI) of the thorax and shoulder girdle was presented at the 99th Annual Meeting of the American Association of Anatomists. These images were the authors' first attempt to correlate the magnetic resonance display of the muscles and soft tissues of the chest in the coronal plane with surface gross anatomy. The original purpose of this study was to introduce the role of magnetic resonance imaging to anatomists, medical students, and the specialty of radiology. However, this approach has been expanded by imaging other sections of the body and applying the display of surface anatomy to augment the teaching of anatomy to surgical oncology, pathology, and kinesiology. This three-part article will display magnetic resonance images and will explain how magnetic imaging of the soft tissues can visually augment the teaching of gross anatomy without dissecting surface tissues.
Images
PMCID: PMC2625920  PMID: 2754751
13.  Anatomy of the abdomen, back, and pelvis as displayed by magnetic resonance imaging: part three. 
In April 1986, magnetic resonance imaging (MRI) of the thorax and shoulder girdle was presented at the 99th Annual Meeting of the American Association of Anatomists. These images were the authors' first attempt to correlate the magnetic resonance display of the muscles and soft tissues of the chest in the coronal plane with surface gross anatomy. The original purpose of this study was to introduce the role of magnetic resonance imaging to anatomists, medical students, and the specialty of radiology. However, this approach has been expanded by imaging other sections of the body and applying the display of surface anatomy to augment the teaching of anatomy to surgical oncology, pathology, and kinesiology. This three-part article will display magnetic resonance images and will explain how magnetic imaging of the soft tissues can visually augment the teaching of gross anatomy without dissecting surface tissues.
Images
PMCID: PMC2626049  PMID: 2769789
14.  Magnetic resonance imaging of chest wall lesions. 
Magnetic resonance imaging (MRI) demonstrates surface anatomy, nerves, and soft tissue pathology. Selective placement of the cursor lines in MRI displays specific anatomy. The MR images can then be used as adjunct in teaching surface anatomy to medical students and to other health professionals. Because the normal surface anatomy could be imaged at UCLA's radiology department, it was decided to image soft tissue abnormalities with MR to assist in patient care. Patients imaged were scheduled for special procedures of the chest or staging lymphangiograms. Patients were placed into categories depending on known diagnosis or interesting clinical presentation. The diagnostic categories included Hodgkin's disease, melanoma, carcinomas (eg, lung or breast), lymphedema, sarcomas, dermatological disorders, and neurological disorders. All images were orchestrated by the radiologist. This article discusses both the teaching and clinical impact on patient care.
Images
PMCID: PMC2627055  PMID: 1920509
15.  Neural Population Tuning Links Visual Cortical Anatomy to Human Visual Perception 
Neuron  2015;85(3):641-656.
Summary
The anatomy of cerebral cortex is characterized by two genetically independent variables, cortical thickness and cortical surface area, that jointly determine cortical volume. It remains unclear how cortical anatomy might influence neural response properties and whether such influences would have behavioral consequences. Here, we report that thickness and surface area of human early visual cortices exert opposite influences on neural population tuning with behavioral consequences for perceptual acuity. We found that visual cortical thickness correlated negatively with the sharpness of neural population tuning and the accuracy of perceptual discrimination at different visual field positions. In contrast, visual cortical surface area correlated positively with neural population tuning sharpness and perceptual discrimination accuracy. Our findings reveal a central role for neural population tuning in linking visual cortical anatomy to visual perception and suggest that a perceptually advantageous visual cortex is a thinned one with an enlarged surface area.
Highlights
•Variability in cortical thickness and surface area has opposite functional impacts•Smaller human visual cortical thickness links to high neural and perceptual acuity•Larger human visual cortical surface area links to high neural and perceptual acuity
Song et al. showed that large brains are not necessarily advantageous. Instead, the two dimensions, thickness and surface area, of human brain have opposite impacts on visual perception. A perceptually advantageous brain is a thinned one with enlarged surface area.
doi:10.1016/j.neuron.2014.12.041
PMCID: PMC4321887  PMID: 25619658
16.  An artifact-robust, shape library-based algorithm for automatic segmentation of inner ear anatomy in post-cochlear-implantation CT 
A cochlear implant (CI) is a device that restores hearing using an electrode array that is surgically placed in the cochlea. After implantation, the CI is programmed to attempt to optimize hearing outcome. Currently, we are testing an image-guided CI programming (IGCIP) technique we recently developed that relies on knowledge of relative position of intracochlear anatomy to implanted electrodes. IGCIP is enabled by a number of algorithms we developed that permit determining the positions of electrodes relative to intra-cochlear anatomy using a pre- and a post-implantation CT. One issue with this technique is that it cannot be used for many subjects for whom a pre-implantation CT was not acquired. Pre-implantation CT has been necessary because it is difficult to localize the intra-cochlear structures in post-implantation CTs alone due to the image artifacts that obscure the cochlea. In this work, we present an algorithm for automatically segmenting intra-cochlear anatomy in post-implantation CTs. Our approach is to first identify the labyrinth and then use its position as a landmark to localize the intra-cochlea anatomy. Specifically, we identify the labyrinth by first approximately estimating its position by mapping a labyrinth surface of another subject that is selected from a library of such surfaces and then refining this estimate by a standard shape model-based segmentation method. We tested our approach on 10 ears and achieved overall mean and maximum errors of 0.209 and 0.98 mm, respectively. This result suggests that our approach is accurate enough for developing IGCIP strategies based solely on post-implantation CTs.
doi:10.1117/12.2043260
PMCID: PMC4112543  PMID: 25076827
Cochlear implant (CI) surgery; CI programming; intra-cochlear anatomy; segmentation; registration
17.  Immobilization of Iron Oxide Magnetic Nanoparticles for Enhancement of Vessel Wall Magnetic Resonance Imaging—An Ex Vivo Feasibility Study 
Bioconjugate Chemistry  2010;21(8):1408-1412.
Emerging data supports a role for negative wall remodeling in the failure of vascular interventions such as vein grafts, yet clinicians/researchers currently lack the ability to temporally/efficiently investigate adventitial surface topography/total vascular wall anatomy in vivo. We established a strategy of immobilizing commercially available iron oxide magnetic nanoparticles (Fe-NPs) onto the surface of human vein conduits to facilitate high-throughput total vascular wall demarcation with magnetic resonance (MR). Binding of activated Fe-NPs to amine groups on the surface of the veins induced a thin layer of negative contrast that differentiated the adventitia from surrounding saline signal in all MR images, enabling delineation of total wall anatomy; this was not possible in simultaneously imaged unlabeled control veins. Under the conditions of this ex vivo experiment, stable covalent binding of Fe-NPs can be achieved (dose-dependent) on human vein surface for MR detection, suggesting a potential strategy for enhancing the ability of MRI to investigate total wall adaptation and remodeling in vein graft failure.
Emerging data supports a role for negative wall remodeling in the failure of vascular interventions such as vein grafts, yet clinicians/researchers currently lack the ability to temporally/efficiently investigate adventitial surface topography/total vascular wall anatomy in vivo. We established a strategy of immobilizing commercially available iron oxide magnetic nanoparticles (Fe-NPs) onto the surface of human vein conduits to facilitate high-throughput total vascular wall demarcation with magnetic resonance (MR).
doi:10.1021/bc100138c
PMCID: PMC2923466  PMID: 20608720
18.  THE UF FAMILY OF REFERENCE HYBRID PHANTOMS FOR COMPUTATIONAL RADIATION DOSIMETRY 
Physics in medicine and biology  2009;55(2):339-363.
Computational human phantoms are computer models used to obtain dose distributions within the human body exposed to internal or external radiation sources. In addition, they are increasingly used to develop detector efficiencies for in-vivo whole-body counters. Two classes of the computational human phantoms have been widely utilized for dosimetry calculation: stylized and voxel phantoms, that describe human anatomy through mathematical surface equations and 3D voxel matrices, respectively. Stylized phantoms are flexible in that changes to organ position and shape are possible given avoidance of region overlap, while voxel phantoms are typically fixed to a given patient anatomy, yet can be proportionally scaled to match individuals of larger or smaller stature, but of equivalent organ anatomy. Voxel phantoms provide much better anatomical realism as compared to stylized phantoms which are intrinsically limited by mathematical surface equations. To address the drawbacks of these phantoms, hybrid phantoms based on non-uniform rational B-spline (NURBS) surfaces have been introduced wherein anthropomorphic flexibility and anatomic realism are both preserved. Researchers at the University of Florida have introduced a series of hybrid phantoms representing the ICRP Publication 89 reference newborn, 15-year, and adult male and female. In this study, six additional phantoms are added to the UF family of hybrid phantoms – those of the reference 1-year, 5-year, and 10-year child. Head and torso CT images of patients whose ages were close to the targeted ages were obtained under approved protocols. Major organs and tissues were segmented from these images using an image processing software, 3D-DOCTOR™. NURBS and polygon mesh surfaces were then used to model individual organs and tissues after importing the segmented organ models to the 3D NURBS modeling software, Rhinoceros™. The phantoms were matched to four reference datasets: (1) standard anthropometric data, (2) reference organ masses from ICRP Publication 89, (3) reference elemental compositions provided in ICRP 89 as well as ICRU Report 46, and (4) reference data on the alimentary tract organs given in ICRP Publications 89 and 100. Various adjustments and refinements to the organ systems of the previously described newborn, 15-year, and adult phantoms are also presented. The UF series of hybrid phantoms retain the non-uniform scalability of stylized phantoms while maintaining the anatomical realism of patient-specific voxel phantoms with respect to organ shape, depth and inter-organ distance. While the final versions of these phantoms are in a voxelized format for radiation transport simulation, their primary format is given as NURBS and polygon mesh surfaces, thus permitting one to sculpt non-reference phantoms using the reference phantoms as an anatomic template.
doi:10.1088/0031-9155/55/2/002
PMCID: PMC2800036  PMID: 20019401
NURBS; voxel; paediatric; hybrid phantom; radiation dosimetry
19.  The effect of a manual instrumentation technique on five types of premolar root canal geometry assessed by microcomputed tomography and three-dimensional reconstruction 
BMC Medical Imaging  2011;11:14.
Background
Together with diagnosis and treatment planning, a good knowledge of the root canal system and its frequent variations is a necessity for successful root canal therapy. The selection of instrumentation techniques for variants in internal anatomy of teeth has significant effects on the shaping ability and cleaning effectiveness. The aim of this study was to reveal the differences made by including variations in the internal anatomy of premolars into the study protocol for investigation of a single instrumentation technique (hand ProTaper instruments) assessed by microcomputed tomography and three-dimensional reconstruction.
Methods
Five single-root premolars, whose root canal systems were classified into one of five types, were scanned with micro-CT before and after preparation with a hand ProTaper instrument. Instrumentation characteristics were measured quantitatively in 3-D using a customized application framework based on MeVisLab. Numeric values were obtained for canal surface area, volume, volume changes, percentage of untouched surface, dentin wall thickness, and the thickness of dentin removed. Preparation errors were also evaluated using a color-coded reconstruction.
Results
Canal volumes and surface areas were increased after instrumentation. Prepared canals of all five types were straightened, with transportation toward the inner aspects of S-shaped or multiple curves. However, a ledge was formed at the apical third curve of the type II canal system and a wide range in the percentage of unchanged canal surfaces (27.4-83.0%) was recorded. The dentin walls were more than 0.3 mm thick except in a 1 mm zone from the apical surface and the hazardous area of the type II canal system after preparation with an F3 instrument.
Conclusions
The 3-D color-coded images showed different morphological changes in the five types of root canal systems shaped with the same hand instrumentation technique. Premolars are among the most complex teeth for root canal treatment and instrumentation techniques for the root canal systems of premolars should be selected individually depending on the 3-D canal configuration of each tooth. Further study is needed to demonstrate the differences made by including variations in the internal anatomy of teeth into the study protocol of clinical RCT for identifying the best preparation technique.
doi:10.1186/1471-2342-11-14
PMCID: PMC3142503  PMID: 21676233
Manual instruments; Microcomputed tomography; Root canal preparation; Root canal system; Three-dimensional imaging
20.  Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology 
Background
Spatial terminology is used in anatomy to indicate precise, relative positions of structures in an organism. While these terms are often standardized within specific fields of biology, they can differ dramatically across taxa. Such differences in usage can impair our ability to unambiguously refer to anatomical position when comparing anatomy or phenotypes across species. We developed the Biological Spatial Ontology (BSPO) to standardize the description of spatial and topological relationships across taxa to enable the discovery of comparable phenotypes.
Results
BSPO currently contains 146 classes and 58 relations representing anatomical axes, gradients, regions, planes, sides, and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. Spatial reasoning is further enhanced in anatomy ontologies by integrating spatial relations such as dorsal_to into class descriptions (e.g., ‘dorsolateral placode’ dorsal_to some ‘epibranchial placode’).
Conclusions
The BSPO is currently used by projects that require standardized anatomical descriptors for phenotype annotation and ontology integration across a diversity of taxa. Anatomical location classes are also useful for describing phenotypic differences, such as morphological variation in position of structures resulting from evolution within and across species.
doi:10.1186/2041-1480-5-34
PMCID: PMC4137724  PMID: 25140222
Anatomy; Spatial relationships; Position; Axes; Reasoning; BSPO; Ontology; Phenotype
21.  Three-Dimensional Virtual Model of the Human Temporal Bone: A Stand-Alone, Downloadable Teaching Tool 
Objective
To develop a three-dimensional virtual model of a human temporal bone based on serial histologic sections.
Background
The three-dimensional anatomy of the human temporal bone is complex, and learning it is a challenge for students in basic science and in clinical medicine.
Methods
Every fifth histologic section from a 14-year-old male was digitized and imported into a general purpose three-dimensional rendering and analysis software package called Amira (version 3.1). The sections were aligned, and anatomic structures of interest were segmented.
Results
The three-dimensional model is a surface rendering of these structures of interest, which currently includes the bone and air spaces of the temporal bone; the perilymph and endolymph spaces; the sensory epithelia of the cochlear and vestibular labyrinths; the ossicles and tympanic membrane; the middle ear muscles; the carotid artery; and the cochlear, vestibular, and facial nerves. For each structure, the surface transparency can be individually controlled, thereby revealing the three-dimensional relations between surface landmarks and underlying structures. The three-dimensional surface model can also be “sliced open” at any section and the appropriate raw histologic image superimposed on the cleavage plane. The image stack can also be resectioned in any arbitrary plane.
Conclusion
This model is a powerful teaching tool for learning the complex anatomy of the human temporal bone and for relating the two-dimensional morphology seen in a histologic section to the three-dimensional anatomy. The model can be downloaded from the Eaton-Peabody Laboratory web site, packaged within a cross-platform freeware three-dimensional viewer, which allows full rotation and transparency control.
doi:10.1097/01.mao.0000188353.97795.c5
PMCID: PMC1805780  PMID: 16791035
Histologic section; Human temporal bone; Surface rendering; Three-dimensional reconstruction
22.  Surgical approaches to the distal radius 
Hand (New York, N.Y.)  2010;6(1):8-17.
Introduction
Fractures of the distal radius are among the most common fractures seen. They encompass a myriad of presentations and fracture patterns that often benefit from various open reduction and internal fixation techniques—including volar plating, dorsal plating, radial plating, intramedullary nailing, and fragment-specific fixation. In order to obtain optimal reduction of these fractures, surgeons require a thorough understanding of the anatomy and various surgical exposures.
Anatomy
The distal radius is surrounded by a soft tissue envelope rich in vascularity and cutaneous innervation. The osseous surface consists of two articular surfaces and three cortical sides covered almost entirely by soft tissue.
Surgical approaches
Approaches to the distal radius can be broadly divided into volar, radial, and dorsal. Visualization of the articular surface can be accomplished best arthroscopically. Arthroscopy can be performed alone or in conjunction with other open approaches to the distal radius.
Summary
This article will review the pertinent anatomy and various surgical approaches in order to facilitate the surgeon’s ability to safely expose a distal radius fracture.
doi:10.1007/s11552-010-9281-9
PMCID: PMC3041890  PMID: 22379433
Distal radius; Exposure; Volar approach; Dorsal approach; Radial approach; Henry’s approach; Thompson’s approach
23.  Portable Document Format File Showing the Surface Models of Cadaver Whole Body 
Journal of Korean Medical Science  2012;27(8):849-856.
In the Visible Korean project, 642 three-dimensional (3D) surface models have been built from the sectioned images of a male cadaver. It was recently discovered that popular PDF file enables users to approach the numerous surface models conveniently on Adobe Reader. Purpose of this study was to present a PDF file including systematized surface models of human body as the beneficial contents. To achieve the purpose, fitting software packages were employed in accordance with the procedures. Two-dimensional (2D) surface models including the original sectioned images were embedded into the 3D surface models. The surface models were categorized into systems and then groups. The adjusted surface models were inserted to a PDF file, where relevant multimedia data were added. The finalized PDF file containing comprehensive data of a whole body could be explored in varying manners. The PDF file, downloadable freely from the homepage (http://anatomy.co.kr), is expected to be used as a satisfactory self-learning tool of anatomy. Raw data of the surface models can be extracted from the PDF file and employed for various simulations for clinical practice. The technique to organize the surface models will be applied to manufacture of other PDF files containing various multimedia contents.
doi:10.3346/jkms.2012.27.8.849
PMCID: PMC3410230  PMID: 22876049
Models, Anatomic; Image Processing, Computer-Assisted; Imaging, Three-Dimensional; User-Computer Interface; Visible Human Projects
24.  Assessment of interfractional variation of the breast surface following conventional patient positioning for whole-breast radiotherapy 
The purpose of this study was to quantify the variability of the breast surface position when aligning whole-breast patients to bony landmarks based on MV portal films or skin marks alone. Surface imaging was used to assess the breast surface position of 11 whole-breast radiotherapy patients, but was not used for patient positioning. On filmed fractions, AlignRT v5.0 was used to capture the patient's surface after initial positioning based on skin marks (28 “preshifts” surfaces), and after treatment couch shifts based on MV films (41 “postshifts” surfaces). Translations and rotations based on surface captures were recorded, as well as couch shifts based on MV films. For nonfilmed treatments, “daily” surface images were captured following positioning to skin marks alone. Group mean and systematic and random errors were calculated for all datasets. Pearson correlation coefficients, setup margins, and 95% limits of agreement (LOA) were calculated for preshifts translations and MV film shifts. LOA between postshifts surfaces and the filmed treatment positions were also computed. All the surface captures collected were retrospectively compared to both a DICOM reference surface created from the planning CT and to an AlignRT reference surface. All statistical analyses were performed using the DICOM reference surface dataset. AlignRT reference surface data was only used to calculate the LOA with the DICOM reference data. This helped assess any outcome differences between both reference surfaces. Setup margins for preshifts surfaces and MV films range between 8.3–12.0 mm and 5.4–13.4 mm, respectively. The largest margin is along the left–right (LR) direction for preshift surfaces, and along craniocaudal (CC) for films. LOA ranges between the preshifts surfaces and MV film shifts are large (12.6–21.9 mm); these decrease for postshifts surfaces (9.8–18.4 mm), but still show significant disagreements between the two modalities due to their focus on different anatomical landmarks (patient's topography versus bony anatomy). Pearson's correlation coefficients further support this by showing low to moderate correlations in the anterior–posterior (AP) and LR directions (0.47–0.69) and no correlation along CC (< 0.15). The use of an AlignRT reference surface compared to the DICOM reference surface does not significantly affect the LOA. Alignment of breast patients based solely on bony alignment may lead to interfractional inconsistencies in the breast surface position. The use of surface imaging tools highlights these discrepancies, and allows the radiation oncology team to better assess the possible effects on treatment quality.
PMCID: PMC4273911  PMID: 25207578
WBRT; surface imaging; patient positioning; MV portal films
25.  Identification of Pleiotropic Genetic Effects on Obesity and Brain Anatomy 
Human heredity  2013;75(0):136-143.
Background/Aims
Obesity is a major contributor to the global burden of chronic disease and disability, though current knowledge of causal biologic underpinnings is lacking. Through the regulation of energy homeostasis and interactions with adiposity and gut signals, the brain is thought to play a significant role in the development of this disorder. While neuroanatomic variation has been associated with obesity, it is unclear if this relationship is influenced by common genetic mechanisms. In this study, we sought genetic components that influence both brain anatomy and body mass index (BMI) to provide further insight into the role of the brain in energy homeostasis and obesity.
Methods
MRI images of brain anatomy were acquired in 839 Mexican American individuals from large extended pedigrees. Bivariate linkage and quantitative analyses were performed in SOLAR.
Results
Genetic factors associated with increased BMI were also associated with reduced cortical surface area and subcortical volume. We identified two genome-wide quantitative trait loci that influenced BMI and ventral diencephalon volume, and BMI and supramarginal gyrus surface area, respectively.
Conclusions
This study represents the first genetic analyses seeking evidence of pleiotropic effects acting on both brain anatomy and BMI. Results suggest that a region on chromosome 17 contributes to the development of obesity, potentially through leptin-induced signaling in the hypothalamus, and that a region on chromosome 3 appears to jointly influences food-related reward circuitry and the supramarginal gyrus.
doi:10.1159/000353953
PMCID: PMC3889074  PMID: 24081229
BMI; obesity; imaging; brain; pleiotropy

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