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Segmentation of 4D cardiac MR images using a probabilistic atlas and the EM algorithm.

In this paper an automatic atlas-based segmentation algorithm for 4D cardiac MR images is proposed. The algorithm is based on the 4D extension of the expectation maximisation (EM) algorithm. The EM algorithm uses a 4D probabilistic cardiac atlas to estimate the initial model parameters and to integrate a priori information into the classification process. The probabilistic cardiac atlas has been constructed from the manual segmentations of 3D cardiac image sequences of 14 healthy volunteers. It provides space and time-varying probability maps for the left and right ventricles, the myocardium, and background structures such as the liver, stomach, lungs and skin. In addition to using the probabilistic cardiac atlas as a priori information, the segmentation algorithm incorporates spatial and temporal contextual information by using 4D Markov Random Fields. After the classification, the largest connected component of each structure is extracted using a global connectivity filter which improves the results significantly, especially for the myocardium. Validation against manual segmentations and computation of the correlation between manual and automatic segmentation on 249 3D volumes were calculated. We used the 'leave one out' test where the image set to be segmented was not used in the construction of its corresponding atlas. Results show that the procedure can successfully segment the left ventricle (LV) (r = 0.96), myocardium (r = 0.92) and right ventricle (r = 0.92). In addition, 4D images from 10 patients with hypertrophic cardiomyopathy were also manually and automatically segmented yielding a good correlation in the volumes of the LV (r = 0.93) and myocardium (0.94) when the atlas constructed with volunteers is blurred.

Algorithms↗

The creation of a brain atlas for image guided neurosurgery using serial histological data.

Digital and print brain atlases have been used with success to help in the planning of neurosurgical interventions. In this paper, a technique presented for the creation of a brain atlas of the basal ganglia and the thalamus derived from serial histological data. Photographs of coronal histological sections were digitized and anatomical structures were manually segmented. A slice-to-slice nonlinear registration technique was used to correct for spatial distortions introduced into the histological data set at the time of acquisition. Since the histological data were acquired without any anatomical reference (e.g., block-face imaging, post-mortem MRI), this registration technique was optimized to use an error metric which calculates a nonlinear transformation minimizing the mean distance between the segmented contours between adjacent pairs of slices in the data set. A voxel-by-voxel intensity correction field was also estimated for each slice to correct for lighting and staining inhomogeneity. The reconstructed three-dimensional (3D) histological volume can be viewed in transverse and sagittal directions in addition to the original coronal. Nonlinear transformations used to correct for spatial distortions of the histological data were applied to the segmented structure contours. These contours were then tessellated to create three-dimensional geometric objects representing the different anatomic regions in register with the histological volumes. This yields two alternate representations (one histological and one geometric) of the atlas. To register the atlas to a standard reference MR volume created from the average of 27 T1-weighted MR volumes, a pseudo-MRI was created by setting the intensity of each anatomical region defined in the geometric atlas to match the intensity of the corresponding region of the reference MR volume. This allowed the estimation of a 3D nonlinear transformation using a correlation based registration scheme to fit the atlas to the reference MRI. The result of this procedure is a contiguous 3D histological volume, a set of 3D objects defining the basal ganglia and thalamus, both of which are registered to a standard MRI data set, for use for neurosurgical planning.

Algorithms↗

A spatially unbiased atlas template of the human cerebellum.

This article presents a new high-resolution atlas template of the human, cerebellum and brainstem, based on the anatomy of 20 young healthy individuals. The atlas is spatially unbiased, i.e., the location of each structure is equal to the expected location of that structure across individuals in MNI space, a result that is cross-validated with an independent sample of 16 individuals. At the same time, the new template preserves the anatomical detail of cerebellar structures through a nonlinear atlas generation algorithm. In comparison to current whole-brain templates, it allows for an improved voxel-by-voxel normalization for functional MRI and lesion analysis. Alignment to the template requires that the cerebellum and brainstem are isolated from the surrounding tissue, a process for which an automated algorithm has been developed. Compared to normalization to the MNI whole-brain template, the new method strongly improves the alignment of individual fissures, reducing their spatial spread by 60%, and improves the overlap of the deep cerebellar nuclei. Applied to functional MRI data, the new normalization technique leads to a 5-15% increase in peak t values and in the activated volume in the cerebellar cortex for movement vs. rest contrasts. This indicates that the new template significantly improves the overlap of functionally equivalent cerebellar regions across individuals. The template and software are freely available as an SPM-toolbox, which also allows users to relate the new template to the annotated volumetric (Schmahmann, J.D., Doyon, J., Toga, A., Petrides, M., Evans, A. (2000). MRI atlas of the human cerebellum. San Diego: Academic Press) and surface-based (Van Essen, D.C. (2002a) Surface-based atlases of cerebellar cortex in the human, macaque, and mouse. Ann. N. Y. Acad. Sci. 978:468-479.) atlas of one individual, the "colin27"-brain.

Adult↗

A three-dimensional digital atlas database of the adult C57BL/6J mouse brain by magnetic resonance microscopy.

A comprehensive three-dimensional digital atlas database of the C57BL/6J mouse brain was developed based on magnetic resonance microscopy images acquired on a 17.6-T superconducting magnet. By using both manual tracing and an atlas-based semi-automatic segmentation approach, T2-weighted magnetic resonance microscopy images of 10 adult male formalin-fixed, excised C57BL/6J mouse brains were segmented into 20 anatomical structures. These structures included the neocortex, hippocampus, amygdala, olfactory bulbs, basal forebrain and septum, caudate-putamen, globus pallidus, thalamus, hypothalamus, central gray, superior colliculi, inferior colliculi, the rest of midbrain, cerebellum, brainstem, corpus callosum/external capsule, internal capsule, anterior commissure, fimbria, and ventricles. The segmentation data were formatted and stored into a database containing three different atlas types: 10 single-specimen brain atlases, an average brain atlas and a probabilistic atlas. Additionally, quantitative group information, such as variations in structural volume, surface area, magnetic resonance microscopy image intensity and local geometry, were computed and stored as an integral part of the database. The database augments ongoing efforts with other high priority strains as defined by the Mouse Phenome Database focused on providing a quantitative framework for accurate mapping of functional, genetic and protein expression patterns acquired by a myriad of technologies and imaging modalities.

Anatomy, Artistic↗

Automatic measurement of the labyrinth using image registration and a deformable inner ear atlas.

RATIONALE AND OBJECTIVES: This article presents a new method for measuring the shape of the cochlea, vestibule, semi-circular canals, and internal auditory canal using image registration and a deformable inner ear atlas. MATERIALS AND METHODS: Computed tomography images of the inner ear are analyzed by placing them into a common orientation and then registering a digital atlas of the inner ear to the data set. The atlas is deformed from its original shape to match the shape of the inner ear in the computed tomography data set using inverse consistent elastic image registration. This process produces an individualized inner ear atlas containing subject-specific measurements and segmentations of the inner ear anatomy in the target computed tomography data set. The shape measurements include the volume and length of the cochlea, vestibule, semi-circular canals, and internal auditory canal; and the angles between the semi-circular canals. RESULTS: A simulated population of inner ear shapes were generated based on the shape of a real population of inner ear shapes and were used to characterize the measurement error of this method. The deformable atlas was used to measure the shape of the left and right inner ear of six individuals. CONCLUSION: Measurement error for 15 of the 24 measurements of our simulated population had an average error of less than 1% and only one measurement had an average error greater than 2.54%. The deformable human inner ear atlas shows promise as a new method for automatically measuring the shape of the labyrinth.

Adult↗

An atlas of forecasted molecular data. 1. Internuclear separations of main-group and transition-metal neutral gas-phase diatomic molecules in the ground state.

Needed spectroscopic data on diatomic molecules can often be found in the superb critical tables of Huber and Herzberg or in the literature published since 1979. Unfortunately, these sources apply to only a fraction of the diatomic species that can exist and so investigators have had to rely on interpolation, additivity, or ad hoc rules to estimate needed values, all of which require other information that is often lacking. This Atlas presents 1001 additional internuclear separations for use until critical tables are available to fill the needs more precisely. The Atlas was produced by mining the data from Huber and Herzberg for trends with least-squares analysis and with neural network software. There are 162 molecules about whose data Huber and Herzberg had no qualifications and whose data were employed for this work; 248 copies of data with low and high magnitudes were added to reduce the effects of frequency. Internuclear separations for 1001 species not found in Huber and Herzberg are presented, and least-squares predictions supplement some of them. The results, i.e., the Atlas, are presented as Table A, Supporting Information. The average error, based on the average of the absolute differences between the predicted values and tabulated values for the molecules having Huber and Herzberg data, is 0.074 A; if each error is expressed as a percent of the forecast to which it pertains, the average of these errors is 2.94%. There are 25 "questionable" data from Huber and Herzberg, not used in the preparation of the Atlas, for which predictions are included in the Atlas. Of these, 14 agree with the predicted internuclear separations to within twice the stated errors. Additional atlases for other properties of diatomic molecules are in preparation.

Journal Article↗

What should we do about Eduard Pernkopf's atlas?

Eduard Pernkopf created a classic anatomy atlas during World War II. He was also an ardent Nazi. Questions have been raised recently about the propriety of using an atlas created by a Nazi and illustrated by dissections of cadavers whose identities are unknown, but who could have been victims of Nazi political terror. To examine the ethical issues involved, the author first reviews recently published work regarding Pernkopf and his atlas, with the caution that facts are few in a debate where emotions run high and opinions abound. He then considers what has been written by bioethicists on the use of scientific data from the Nazi era and how those arguments might apply to Pernkopf and his atlas. Important questions remain, however. For example, are scientific data tainted by their associations with Nazism, or should such data (including the atlas) be assessed on their own merits, separate from the persons and ideologies involved in their creation? Finally, the author offers his own perspective as a young gross anatomist and physician. He argues that rejecting the hateful beliefs of Pernkopf and his fellow Nazis does not necessitate rejecting the elegant anatomic images they produced. The author further suggests that use of the atlas is itself the most fitting tribute to those who died for it, whether they were victims of Nazi repression or not. Those cadavers not only teach anatomy, they "can remind us of suffering not only in the past but in the present, that we may be more compassionate physicians, more compassionate citizens of the world."

Anatomy, Artistic↗

Automated atlas integration and interactive three-dimensional visualization tools for planning and guidance in functional neurosurgery.

Many critical functionally distinct subcortical structures are not distinguishable on anatomical magnetic resonance imaging (MRI) scans. In order to provide the neurosurgeon with this missing information, a deformable volumetric atlas of the basal ganglia and thalamus has been created from the Schaltenbrand and Wahren atlas of cryogenic slices. The volumetric atlas can be automatically deformed to an individual patient's MRI. To facilitate the clinical use of the atlas, a visualization platform has been developed for preoperative and intraoperative use which permits manipulation of the merged atlas and MRI data sets in two- and three-dimensional views. The platform includes graphical tools which allow the visualization of projections of a leukotome and other surgical tools with respect to the atlas data, as well as preregistered images from any other imaging modality. In addition, a graphical interface has been designed to create custom virtual lesions using computer models of neurosurgical tools for intraoperative planning. To date this system has been employed as an adjunct to over 30 functional neurosurgical cases including surgery for movement disorders.

Algorithms↗

Informatics in Radiology (infoRAD): three-dimensional atlas of the brain anatomy and vasculature.

Of the existing atlases of the brain anatomy and cerebrovasculature, none integrates the anatomy and vasculature by providing for direct manipulation of three-dimensional (3D) cerebral models. An atlas-based application was developed in four steps: (a) construction of 3D anatomic models, (b) construction of 3D vascular models, (c) interactive spatial coregistration of the anatomic and vascular models, and (d) development of functionality and a user interface for the application. Three-dimensional anatomic models were imported from an electronic brain atlas database derived from classic print atlases. A novel vascular modeling technique was developed and applied to create a vascular atlas from magnetic resonance angiographic data. The use of 3D polygonal models allows smooth navigation (rotation, zooming, panning) and interactive labeling of anatomic structures and vascular segments. This application enables the user to examine 3D anatomic structures and 3D cerebral vasculature and to gain a better understanding of the relationships between the two. The combined anatomic-vascular atlas is a user-friendly neuroeducational tool that is useful for medical students and neuroscience researchers as well as for educators in preparing teaching materials.

Brain↗

Anatomical targeting in functional neurosurgery by the simultaneous use of multiple Schaltenbrand-Wahren brain atlas microseries.

This paper presents a novel approach for the use of the Atlas for Stereotaxy of the Human Brain by Schaltenbrand and Wahren [Stuttgart, Thieme, 1977] for anatomical targeting in functional neurosurgery. We propose to use simultaneously all three electronic axial, coronal and sagittal mutually coregistered Schaltenbrand-Wahren brain atlas microseries. The printed atlas microseries are digitized, extended to cover both hemispheres, contoured, labeled, organized into atlas volumes, and mutually coregistered. The electronic atlas is interactively registered with the data by using the three-dimensional Talairach proportional grid system transformation, followed up by local warping in the region of interest based on any clearly visible landmarks. The detailed targeting steps for pallidotomy, thalamotomy and subthalamotomy are formulated. The potential of this approach is to increase the accuracy of target definition, to decrease the time of the procedure by reducing the number of microelectrode tracts, and to give an extra degree of confidence to the neurosurgeon. The advantages of the approach and the limitations of the Schaltenbrand-Wahren atlas are discussed.

Anatomy, Artistic↗

Computer-aided interpretation of SPECT images of the brain using an MRI-derived 3D neuro-anatomical atlas.

Nuclear medicine images have comparatively poor spatial resolution, making it difficult to relate the functional information which they contain to precise anatomical structures. A 3D neuro-anatomical atlas has been generated from the MRI data set of a normal, healthy volunteer to assist in the interpretation of nuclear medicine scans of the brain. Region growing and edge-detection techniques were used to semi-automatically segment the data set into the major tissue types within the brain. The atlas was then labelled interactively by marking points on each 2D slice. Anatomical structures useful in the interpretation of SPECT images were labelled. Additional, more detailed information corresponding to these structures is provided via an interactive index which allows access to images, diagrams and explanations. Registration of patient SPECT studies with the atlas is accomplished by using the position of the skull vertex and four external fiducial markers attached to the skin surface. The 3D coordinates determined from these points are used to calculate the transformation required to rotate, scale and translate the SPECT data, in 3D, to match the atlas. Corresponding 2D slices from the two 3D data sets are then displayed side-by-side on a computer screen. A cursor linking the two images allows the delineation of regions of interest (ROIs) in the SPECT scan based on anatomical structures identified from the atlas. Conversely regions of abnormal isotope distribution in the SPECT image can be localized by reference to corresponding structures in the atlas.

Brain↗

An international dermatological image atlas on the WWW: practical use for undergraduate and continuing medical education, patient education and epidemiological research.

We describe the development of an image database DOIA (Dermatological OnlIne Atlas) and present several spin-off projects using images of the atlas, e.g. student education using the atlas including results of an questionnaire evaluating computer-literacy, prerequisites and interests of students for using computers and the World-Wide-Web (WWW), a patient information system and an experiment to collect epidemiological data from patients with dermatological diseases via WWW. The database, available on the WWW at http:@www.derma.med.uni-erlangen.de, contains about 3,000 clinical images covering more than 540 dermatological diagnoses. It is designed for worldwide use; international submissions are encouraged. One aim of the project is to compile an international reference for dermatological images, containing images of high educational quality and also covering conditions on different skin types and rare diagnoses which are not commonly illustrated in ordinary textbooks. All images were originally mapped to the Erlanger Diagnosis Code, which is a proprietary modified ICD-9 key, later also to the UMLS (Unified Medical Language System). In addition, images are described with keys for the location, physical attributes of the location and clinical and histopathological features of the lesion. In order to facilitate the integration of the atlas into other web-based medical resources and to allow easy access to additional information, the Erlanger Diagnosis Code was mapped to the CUIs (unique concept identifiers) of the UMLS Metathesaurus. One purpose of the UMLS is to allow conversion of terms from one controlled medical vocabulary to another, thus, mapping of our diagnosis code to the UMLS CUIs allows simultaneous search for a given diagnosis in a number of other databases and also access to our image database from other databases. Mapping was successful for 619 out of 1383 dermatological diagnosis terms. For images with these diagnoses we are able to provide a hyperlink to other databases available on the Internet, such as MEDLINE, PDQ and OMIM, with automatic retrieval using the preferred vocabulary of the respective database. By grouping all diagnoses into sets with similar morphologies we further integrated a differential diagnosis mode. In order to educate patients via the Internet, a separate patient information system has been developed, using images of the electronic atlas. As an experiment to explore the feasibility of the Internet to gather epidemiological data from patients, users are asked to complete an electronic questionnaire covering signs for atopy. We conclude that an online image atlas has multiple educational, clinical and research applications.

Computer-Assisted Instruction↗

A computerized brain atlas: construction, anatomical content, and some applications.

An adjustable computerized atlas of the human brain has been developed, which can be adapted to fit individual anatomy. It is primarily intended for positron emission tomography (PET) but may also be used for single photon emission CT, transmission CT, magnetic resonance imaging, and neuroimaging-based procedures, such as stereotactic surgery and radiotherapy. The atlas is based on anatomical information obtained from brains fixed in situ soon after death. All structures have been drawn in on digitized photos of slices from one cryosectioned brain. The definition and classification of the anatomical structures and divisions are in agreement with the standard textbooks of anatomy, and the nomenclature is that of the Nomina Anatomica of 1965. The boundaries of the cortical cytoarchitectonic areas (Brodmann areas) have been determined using information from several sources, since three-dimensional literature data on their distribution are incomplete, scarce, and partly contradictory. However, no analysis of the cytoarchitectonics of the atlas brain itself has been undertaken. At present the data base contains three-dimensional representations of the brain surface, the ventricular system, the cortical gyri and sulci, as well as the Brodmann cytoarchitectonic areas. The major basal ganglia, the brain stem nuclei, the lobuli of the vermis, and the cerebellar hemispheres are also included. The computerized atlas can be used to improve the quantification and evaluation of PET data in several ways. For instance, it can serve as a guide in selecting regions of interest. It may also facilitate comparisons of data from different individuals or groups of individuals, by applying the inverse atlas transformation to PET data volume, thus relating the PET information to the anatomy of the reference atlas rather than to the patient's anatomy. Reformatted PET data from individuals can thus be averaged, and averages from different categories or different functional states of patients can be compared.

Anatomy, Artistic↗

Applications of a computerized adjustable brain atlas in positron emission tomography.

A computerized brain atlas, adjustable to the patient's anatomy, has been developed. It is primarily intended for use in positron emission tomography (PET), but may also be employed in other fields utilizing neuro-imaging, such as stereotactic surgery. The atlas is based on anatomic information obtained from digitized cryosectioned cadaver brains. It can be adjusted to fit a wide range of individual brains with reasonable accuracy. The corresponding transformation is chosen so that the modified atlas agrees with a set of CT or MR images of the patient. The computerized atlas can be used to facilitate and improve the quantification and evaluation of PET data by: enabling the merging and comparison of results from different individuals or groups of individuals; serving as a vehicle in the comparison of different examinations of the same patient, thus reducing the need of reproducible fixation systems; supplying external information to be used in the image reconstruction, such as proper three-dimensional regions of interest; improving the attenuation and scatter corrections; helping to select suitable patient orientation during the PET study. By applying the inverse atlas transformation to the PET data volume it is possible to relate the PET information to the anatomy of the reference atlas. Reformatted PET data from different patients can thus be averaged, and averages from different categories of patients can be compared. The method will facilitate the identification of statistically significant differences in the PET information from different groups of patients.

Brain↗

Stereotactic PET atlas of the human brain: aid for visual interpretation of functional brain images.

UNLABELLED: In the routine analysis of functional brain images obtained by PET, subjective visual interpretation is often used for anatomic localization. To enhance the accuracy and consistency of the anatomic interpretation, a PET stereotactic atlas and localization approach was designed for functional brain images. METHODS: The PET atlas was constructed from a high-resolution [18F]fluorodeoxyglucose (FDG) image set of a normal volunteer (a 41-yr-old woman). The image set was reoriented stereotactically, according to the intercommissural (anterior and posterior commissures) line and transformed to the standard stereotactic atlas coordinates. Cerebral structures were annotated on the transaxial planes by using a proportional grid system and surface-rendered images. The stereotactic localization technique was applied to image sets from patients with Alzheimer's disease, and areas of functional alteration were localized visually by referring to the PET atlas. RESULTS: Major brain structures were identified on both transaxial planes and surface-rendered images. In the stereotactic system, anatomic correspondence between the PET atlas and stereotactically reoriented individual image sets of patients with Alzheimer's disease facilitated both indirect and direct localization of the cerebral structures. CONCLUSION: Because rapid stereotactic alignment methods for PET images are now available for routine use, the PET atlas will serve as an aid for visual interpretation of functional brain images in the stereotactic system. Widespread application of stereotactic localization may be used in functional brain images, not only in the research setting, but also in routine clinical situations.

Adult↗

First cervical vertebra (atlas) fracture mechanism studies using finite element method.

Injury mechanisms and stress distribution patterns are important in the clinical evaluation of spinal injuries. Recognition and interpretation of the failure patterns help to determine spinal instability and consequently the choice of treatment. Although, the biomechanics responses of the atlas have received much attention, it has not been investigated using theoretical modeling. Mathematical techniques such as finite element model will provide further understanding to the injury mechanisms of the atlas, which is important for the prevention, diagnosis, and treatment of spinal injuries. In the present study, a detailed three-dimensional finite element model of the human atlas (C1) was constructed, with the geometrical data obtained using a three-dimensional digitizer. Anterior arch, superior/inferior articular processes, transverse processes, posterior arch and posterior tubercule were modeled using eight-noded brick elements. Using the material properties from literature, the 7808-finite element model was exercised under three simulated axial compressive mode of pressure loading and boundary conditions to investigate the sites of failure reported in vivo and in vitro. This report demonstrates high concentration of localized stress at the anterior and posterior archs of the atlas, which agrees well with those reported in the literature. Furthermore, under simulated hyperextension, our results agreed well with the experimental findings, which show that the groove of the posterior arch is subjected to enormous bending moment. The close agreement of the failure location provided confidence to perform further analysis and in vitro experiments. These results may be potentially used to supplement experimental research in understanding the clinical biomechanics of the atlas.

Aged↗

A global livestock production and health atlas (GLiPHA) for interactive presentation, integration and analysis of livestock data.

An interactive electronic atlas has been developed with the purpose of providing a scaleable overview of spatial and temporal variation in animal production and health-related information for decision and policy makers in national and international institutions. The information contained in the atlas is currently managed and presented using the Key Indicators Mapping System (KIMS), and will also be integrated using the Key Indicators Database System (KIDS). Both systems were developed by the World Agricultural Information Centre of the FAO (FAO-WAICENT), the former as a stand-alone application and the latter for access via the Internet. Components of the atlas include vector maps, livestock disease and production databases, rules for country-level disease risk classification and 'disease cards' containing basic background information on diseases included in the atlas. The disease data is currently based primarily on Office International des Epizooties (OIE) disease reports, and the livestock production data on the FAO-WAICENT database. The atlas is highly interactive and allows visual presentation of information using maps, tables and charts. It also contains links to relevant resource information on the Internet. Diseases covered in the animal health layer include most OIE List A diseases and a subset of OIE List B diseases. Extensive analyses have been conducted to develop a set of qualitative and semi-quantitative criteria that allow improved disease status classifications based on 5-years cumulative OIE disease reports, and official disease control declarations. Classification rules were determined depending on the epidemiological features of each disease and considering spatial heterogeneity of disease presence in local regions.

Animal Diseases↗

Atlas morphology in relation to craniofacial morphology and head posture.

The associations between dimensions of the first cervical vertebra, atlas, and a representative set of craniofacial and postural variables were studied on cephalometric radiographs of a sample of 103 adult males aged 22-30 years, recorded in the natural head position (mirror position). Atlas morphology was expressed by nine variables, linear and angular craniofacial dimensions by 27 variables, and head and cervical posture by seven variables. A pattern of low but significant correlations was found. Although the correlations were low, the study confirmed that the dimensions of the atlas vertebra reflect associations between cranio-cervical posture and craniofacial morphology. Negative correlations were found between the height of the posterior arch of atlas and the inclination of the mandible and the maxilla to the anterior cranial base. Low positive correlations between the height of the anterior arch and vertical facial dimensions reflect the general co-ordination of the vertical growth of the face and the cervical column. Moreover, the pattern of correlations between the atlanto-cranial angle and facial morphology suggests that in changes of the cranio-cervical angle, atlas follows the cervical column.

Adult↗