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At least 199 records · Page 11Linked to original sources
PubMed2005

Retrospective cross-evaluation of an histological and deformable 3D atlas of the basal ganglia on series of Parkinsonian patients treated by deep brain stimulation.

In functional neurosurgery, there is a growing need for accurate localization of the functional targets. Since deep brain stimulation (DBS) of the Vim thalamic nucleus has been proposed for the treatment of Parkinson's disease, the target has evolved toward the globus pallidus and subthalamic nucleus (STN) and the therapeutic indications have enlarged to include psychiatric disorders such as Tourette syndrome or obsessive compulsive disorders. In these pathologies, the target has been restrained to smaller functional subterritories of the basal ganglia, requiring more refined techniques to localize smaller and smallerbrain regions, often invisible in routine clinical MRI. Different strategies have been developed to identify such deep brain targets. Direct methods can identify structures in the MRI itself, but only the larger ones. Indirect methods are based on the use of anatomical atlases. The present strategy comprised a 3D histological atlas and the MRI of the same brain specimen, and deformation methodology developped to fit the atlas toward the brain of any given patient. In this paper, this method is evaluated in the aim of being applied to further studies of anatomo-clinical correlation. The accuracy of the method is first discussed, followed by the study of short series of Parkinsonian patients treated by DBS, allowing to compare the deformed atlas with various per- and post-operative data.

Basal Ganglia↗
PubMed2005

Unbiased atlas formation via large deformations metric mapping.

The construction of population atlases is a key issue in medical image analysis, and particularly in brain mapping. Large sets of images are mapped into a common coordinate system to study intra-population variability and inter-population differences, to provide voxel-wise mapping of functional sites, and to facilitate tissue and object segmentation via registration of anatomical labels. We formulate the unbiased atlas construction problem as a Fréchet mean estimation in the space of diffeomorphisms via large deformations metric mapping. A novel method for computing constant speed velocity fields and an analysis of atlas stability and robustness using entropy are presented. We address the question: how many images are required to build a stable brain atlas?

Algorithms↗
PubMed2002

[First descriptions in the "International atlas of rare skin diseases" of 1886].

In the history of dermatology, we find an outstanding example of scientific collaboration of leading dermatologists leading to an international publication in the late 19th century. Published by Malcolm Morris, Paul Gerson Unna, Henry-Camille Chrysostome Leloir and Louis Adolphus Duhring, the "International Atlas of Rare Skin Diseases" focused on rare and unique cases in dermatology. This concept, extraordinary for the time of publication, was found to be very successful. Numerous first descriptions are found in the "International Atlas", such as porokeratosis of Mibelli, acanthosis nigricans of Pollitzer and Janovsky and also psorospermosis of Darier. The focus on distinct and detailed descriptions to promote progress in the science of dermatology sets this effort apart from all previous atlases. Therefore, the "International Atlas was one of the first steps leading to the modern concepts of scientific publication in dermatology.

Anatomy, Artistic↗
PubMed2001

Probabilistic approaches for atlasing normal and disease-specific brain variability.

The extreme variability in the structural conformation of the human brain poses significant challenges for the creation of population-based atlases. The ability to statistically and visually compare and contrast brain image data from multiple individuals is essential to understanding normal variability within a particular population as well as differentiating normal from diseased populations. This paper introduces the application of probabilistic atlases that describe specific subpopulations, measures their variability and characterizes the structural differences between them. Utilizing data from structural MRI, we have built atlases with defined coordinate systems creating a framework for mapping data from functional, histological and other studies of the same population. This paper describes the basic approach and a brief description of the underlying mathematical constructs that enable the calculation of probabilistic atlases and examples of their results from several different normal and diseased populations.

Brain↗
PubMed1991

An atlas of the prenatal mouse brain: gestational day 14.

A prenatal atlas of the mouse brain is presently unavailable and is needed for studies of normal and abnormal development, using techniques including immunocytochemistry and in situ hybridization. This atlas will be especially useful for researchers studying transgenic and mutant mice. This collection of photomicrographs and corresponding drawings of Gestational Day (GD) 14 mouse brain sections is an excerpt from a larger atlas encompassing GD 12-18. In composing this atlas, available published studies on the developing rodent brain were consulted to aid in the detailed labeling of embryonic brain structures. C57Bl/6J mice were mated for 1 h, and the presence of a copulation plug was designated as GD 0. GD 14 embryos were perfused transcardially with 4% paraformaldehyde in 0.1 M phosphate buffer and embedded in paraffin. Serial sections (10 microns thickness) were cut through whole heads in sagittal and horizontal planes. They were stained with hematoxylin and eosin and photographed. Magnifications were 43X and 31X for the horizontal and sagittal sections, respectively. Photographs were traced and line drawings prepared using an Adobe Illustrator on a Macintosh computer.

Animals↗
PubMed2005

Atlas-based automatic segmentation of MR images: validation study on the brainstem in radiotherapy context.

PURPOSE: Brain tumor radiotherapy requires the volume measurements and the localization of several individual brain structures. Any tool that can assist the physician to perform the delineation would then be of great help. Among segmentation methods, those that are atlas-based are appealing because they are able to segment several structures simultaneously, while preserving the anatomy topology. This study aims to evaluate such a method in a clinical context. METHODS AND MATERIALS: The brain atlas is made of two three-dimensional (3D) volumes: the first is an artificial 3D magnetic resonance imaging (MRI); the second consists of the segmented structures in this artificial MRI. The elastic registration of the artificial 3D MRI against a patient 3D MRI dataset yields an elastic transformation that can be applied to the labeled image. The elastic transformation is obtained by minimizing the sum of the square differences of the image intensities and derived from the optical flow principle. This automatic delineation (AD) enables the mapping of the segmented structures onto the patient MRI. Parameters of the AD have been optimized on a set of 20 patients. Results are obtained on a series of 6 patients' MRI. A comprehensive validation of the AD has been conducted on performance of atlas-based segmentation in a clinical context with volume, position, sensitivity, and specificity that are compared by a panel of seven experimented physicians for the brain tumor treatments. RESULTS: Expert interobserver volume variability ranged from 16.70 cm(3) to 41.26 cm(3). For patients, the ratio of minimal to maximal volume ranged from 48% to 70%. Median volume varied from 19.47 cm(3) to 27.66 cm(3) and volume of the brainstem calculated by AD varied from 17.75 cm(3) to 24.54 cm(3). Medians of experts ranged, respectively, for sensitivity and specificity, from 0.75 to 0.98 and from 0.85 to 0.99. Median of AD were, respectively, 0.77 and 0.97. Mean of experts ranged, respectively, from 0.78 to 0.97 and from 0.86 to 0.99. Mean of AD were, respectively, 0.76 and 0.97. CONCLUSIONS: Results demonstrate that the method is repeatable, provides a good trade-off between accuracy and robustness, and leads to reproducible segmentation and labeling. These results can be improved by enriching the atlas with the rough information of tumor or by using different laws of deformation for the different structures. Qualitative results also suggest that this method can be used for automatic segmentation of other organs such as neck, thorax, abdomen, pelvis, and limbs.

Algorithms↗
PubMed2004

Precentral gyrus discrepancy in electronic versions of the Talairach atlas.

Electronic versions of the atlas of Talairach and Tournoux, including the Talairach Daemon and the official versions published by Thieme, contain a discrepant region of the precentral gyrus on axial slice +35 mm that extends far forward into the frontal lobe. This area is anatomically incorrect and internally inconsistent within the digital atlas software applications using their multiplanar cross-referencing tools. By cross-referencing the axial, sagittal, and coronal plates from the original printed atlas, we demonstrate that the discrepant area should be labeled middle frontal gyrus. The mislabeled portion encompasses a 3 x 1.5-cm region in the axial plane and has significant implications for sensorimotor studies that rely on the digital atlases for anatomic labeling.

Brain Mapping↗
PubMed2006

The atlas of complication incidence: a proposal for a new standard for reporting the results of radiotherapy protocols.

We present a new method of reporting the results of radiotherapy protocols. The dose-volume atlas of complication incidence is a comprehensive and unbiased summary of the dose-volume exposures and complications occurring in patients after treatment. This new tool provides clear and systematic information about the safety of regions of dose-volume exposure previously treated that can be used when considering new treatments. Actuarial and model-dependent versions of the atlas are described. By using the raw data in the appropriate forms of the atlas, logistic regression, Kaplan-Meier, and Cox proportional hazards analysis can be performed, allowing for the independent calculation of dose-volume response. The data required are simple enough that provided compatible definitions of dose, volume, and complications are used, atlases from different protocols are potentially additive, facilitating the meta-analysis of inter-interinstitutional data. If this method were adopted as a standard for reporting the outcome of treatment protocols, a potentially synergistic increase in the utility of each protocol could result.

Clinical Protocols↗
PubMed1994

Atlas of paced body surface QRS integral maps for localization of the site of origin of postinfarction ventricular tachycardia.

Current mapping during radiofrequency (RF) catheter ablation of postinfarction ventricular tachycardia (VT) is based primarily on the use of single-site mapping techniques. Although such techniques are highly suitable for distinguishing the ultimate site where RF energy is delivered by enabling detailed localization of the exit site or critical component of the VT reentrant circuit, they are time-consuming and inefficient for initial rapid identification of the arrhythmogenic target area. This study features the design and preliminary clinical application of a new noninvasive method that is aimed at speeding up the initial phase of the VT mapping procedure. This method is based on the use of an atlas of 62-lead body surface QRS integral map patterns that was previously developed using left ventricular pace mapping in patients with remote anterior or inferior myocardial infarction. The atlas contains 18 and 22 different paced QRS integral map patterns obtained in patients with previous anterior or inferior myocardial infarction, respectively. Each specific QRS pattern in the atlas provides a unique infarct-specific spatial electrocardiographic representation of the onset of ectopic ventricular activation in a circumscribed endocardial segment of the left ventricle. Localization of the segment of VT origin is obtained by visually or mathematically comparing the QRS integral map recorded during VT with one of the two sets of paced QRS integral maps contained within the atlas with the purpose of selecting the best matching paced QRS integral map pattern.(ABSTRACT TRUNCATED AT 250 WORDS)

Body Surface Potential Mapping↗
PubMed2001

Mapping visual cortex in monkeys and humans using surface-based atlases.

We have used surface-based atlases of the cerebral cortex to analyze the functional organization of visual cortex in humans and macaque monkeys. The macaque atlas contains multiple partitioning schemes for visual cortex, including a probabilistic atlas of visual areas derived from a recent architectonic study, plus summary schemes that reflect a combination of physiological and anatomical evidence. The human atlas includes a probabilistic map of eight topographically organized visual areas recently mapped using functional MRI. To facilitate comparisons between species, we used surface-based warping to bring functional and geographic landmarks on the macaque map into register with corresponding landmarks on the human map. The results suggest that extrastriate visual cortex outside the known topographically organized areas is dramatically expanded in human compared to macaque cortex, particularly in the parietal lobe.

Animals↗
PubMedDate not supplied

An Internet atlas of mouse development.

A prototype two- and three-dimensional color atlas of mouse development is described. The prototype has been developed using two embryos, a 13.5 d normal mouse embryo and a PATCH mutant embryo of the same age. Serial sections of the embryos, with an external registration marker system, introduced into the paraffin embedding process, were prepared by standard histological methods. For the 2D atlas, color images were digitized from 100 consecutive sections of the normal embryo. For the 3D atlas, 300 gray scale images digitized from the mutant embryo were conformally warped and reconstructed into a 3D volume dataset. The external fiducial system facilitated the three-dimensional reconstruction by providing accurate registration of consecutive images and also allowed for precise spatial calibration and the correction for warping artifacts. The atlases, with their associated anatomical knowledge base, will be integrated into a multimedia on-line information resource via the Internet's World Wide Web (WWW) using an enhanced (patent pending, Eòlas Technologies) version of the Mosaic WWW browser program from the National Center for Supercomputer Applications. These programs will provide research biologists with a set of advanced tools to analyze normal and abnormal development.

Anatomy, Artistic↗
PubMed2003

An automated method for neuroanatomic and cytoarchitectonic atlas-based interrogation of fMRI data sets.

Analysis and interpretation of functional MRI (fMRI) data have traditionally been based on identifying areas of significance on a thresholded statistical map of the entire imaged brain volume. This form of analysis can be likened to a "fishing expedition." As we become more knowledgeable about the structure-function relationships of different brain regions, tools for a priori hypothesis testing are needed. These tools must be able to generate region of interest masks for a priori hypothesis testing consistently and with minimal effort. Current tools that generate region of interest masks required for a priori hypothesis testing can be time-consuming and are often laboratory specific. In this paper we demonstrate a method of hypothesis-driven data analysis using an automated atlas-based masking technique. We provide a powerful method of probing fMRI data using automatically generated masks based on lobar anatomy, cortical and subcortical anatomy, and Brodmann areas. Hemisphere, lobar, anatomic label, tissue type, and Brodmann area atlases were generated in MNI space based on the Talairach Daemon. Additionally, we interfaced these multivolume atlases to a widely used fMRI software package, SPM99, and demonstrate the use of the atlas tool with representative fMRI data. This tool represents a necessary evolution in fMRI data analysis for testing of more spatially complex hypotheses.

Brain↗
PubMed2002

The Atlas mountains as a biogeographical divide in North-West Africa: evidence from mtDNA evolution in the Agamid lizard Agama impalearis.

Since the early Miocene there have been several physical events within NW Africa that are likely to have had a major impact on its faunal diversity. Phylogeographical studies will shed new light on the biogeography of the region. We analysed mitochondrial DNA diversity in the agamid lizard Agama impalearis (also called A. bibronii) based on sequences from mitochondrial genes with very different evolutionary rates (16S rRNA and ND2). Well-supported topologies of rooted maximum parsimony trees (with a Laudakia outgroup) and unrooted haplotype networks indicated two major clades with similar branch lengths. These clades have non-overlapping distributions representing respective areas to the North and West and South and East of the Atlas mountain chain and each could be given full species recognition. Nested clade analyses indicate that historical and possible present-day allopatry account for the primary phylogeographic pattern. Further evidence is provided by the estimated timing of cladogenesis, based on calibration of evolutionary rates in the ND2 gene of another continental Agamid. Sequence divergence between clades corresponds to 8.5-9.4mya, coinciding with the main period of orogenic uplift of the Atlas. Additional evidence of cladogenesis by allopatric fragmentation is also detected within the North/West Atlas clade, although contiguous range expansion is the most predominant explanation of more recent phylogeographic effects in this species. Miocene vicariance mediated by the Atlas may provide a general explanation of intra- and interspecific biogeographical patterns in NW African species.

Africa, Northern↗
PubMed2001

Talairach-Tournoux brain atlas registration using a metalforming principle-based finite element method.

In this paper, a novel non-rigid registration method is proposed for registration of the Talairach-Tournoux brain atlas with MRI images and the Schaltenbrand-Wahren brain atlas. A metalforming principle-based finite element method with the large deformation problem is used to find the local deformation, in which finite element equations are governed by constraints in the form of displacements derived from the correspondence relationship between extracted feature points. Some detectable substructures, such as the cortical surface, ventricles and corpus callosum, are first extracted from MRI, forming feature points which are classified into different groups. The softassign method is used to establish the correspondence relationship between feature points within each group and to obtain the global transformation concurrently. The displacement constraints are then derived from the correspondence relationship. A metalforming principle-based finite element method with the large deformation problem is used in which finite element equations are reorganized and simplified by integrating the displacement constraints into the system equations. Our method not only matches the model to the data efficiently, but also decreases the degrees of freedom of the system and consequently reduces the computational cost. The method is illustrated by matching the Talairach-Tournoux brain atlas to MRI normal and pathological data and to the Schaltenbrand-Wahren brain atlas. We compare the results quantitatively between the force assignment-based method and the proposed method. The results show that the proposed method yields more accurate results in a fraction of the time taken by the previous method.

Algorithms↗
PubMed1997

Detection, visualization and animation of abnormal anatomic structure with a deformable probabilistic brain atlas based on random vector field transformations.

This paper describes the design, implementation and preliminary results of a technique for creating a comprehensive probabilistic atlas of the human brain based on high-dimensional vector field transformations. The goal of the atlas is to detect and quantify distributed patterns of deviation from normal anatomy, in a 3-D brain image from any given subject. The algorithm analyzes a reference population of normal scans and automatically generates color-coded probability maps of the anatomy of new subjects. Given a 3-D brain image of a new subject, the algorithm calculates a set of high-dimensional volumetric maps (with typically 384(2) x 256 x 3 approximately 10(8) degrees of freedom) elastically deforming this scan into structural correspondence with other scans, selected one by one from an anatomic image database. The family of volumetric warps thus constructed encodes statistical properties and directional biases of local anatomical variation throughout the architecture of the brain. A probability space of random transformations, based on the theory of anisotropic Gaussian random fields, is then developed to reflect the observed variability in stereotaxic space of the points whose correspondences are found by the warping algorithm. A complete system of 384(2) x 256 probability density functions is computed, yielding confidence limits in stereotaxic space for the location of every point represented in the 3-D image lattice of the new subject's brain. Color-coded probability maps are generated, densely defined throughout the anatomy of the new subject. These indicate locally the probability of each anatomic point being unusually situated, given the distributions of corresponding points in the scans of normal subjects. 3-D MRI and high-resolution cryosection volumes are analyzed from subjects with metastatic tumors and Alzheimer's disease. Gradual variations and continuous deformations of the underlying anatomy are simulated and their dynamic effects on regional probability maps are animated in video format (on the accompanying CD-ROM). Applications of the deformable probabilistic atlas include the transfer of multi-subject 3-D functional, vascular and histologic maps onto a single anatomic template, the mapping of 3-D atlases onto the scans of new subjects, and the rapid detection, quantification and mapping of local shape changes in 3-D medical images in disease and during normal or abnormal growth and development.

Anatomy, Cross-Sectional↗
PubMed2000

Far-infrared spectroscopy of CH3OD in highly excited torsional states and the atlas of the Fourier transform spectra in the range 200-350 cm(-1).

The high resolution Fourier transform far-infrared (FIR) spectrum of the torsion rotation band of CH3OD has been analyzed for the highly excited torsion states (n > or = 2) in the vibrational ground state. The spectrum shows splitting of the lines due to strong torsional-rotational-vibrational interactions in the molecule. Assignments were possible for rotational sub-bands in the torsional state as high as n = 4 and for K values up to 8 and J values of up to approximately 30 in most cases, for all the symmetry species. For the third excited torsional state n = 3 assignments were possible to K = 10. The data were analyzed with the help of the energy expansion model, which has been proven very successful in methanol. The state dependent expansion parameters are presented. These molecular parameters were able to reproduce the observed wavenumbers almost to within experimental accuracy of 0.0002 cm(-1) for clean unblended lines. These expansion coefficients should prove valuable in the calculation of precise energy values for excited torsional states up to n = 4, which is way above the torsional barrier. The detailed high-resolution spectral atlas of CH3OD has been presented in the range 200-350 cm(-1). This atlas is an extension of our earlier atlas in the range 20-205 cm(-1). The availability of this atlas in the journal will be very valuable for spectroscopists and astrophysicists seeking information in the infrared (IR) region in the laboratory and in outer space.

Deuterium↗
PubMed2001

Atlas-based segmentation of bone structures to support the virtual planning of hip operations.

Two 3-D digitised atlases of a female and a male pelvis were generated to support the virtual 3-D planning of hip operations. The anatomical atlases were designed to replace the interactive, time-consuming pre-processing steps for the virtual operation planning. Each atlas consists of a labelled reference CT data set and a set of anatomical point landmarks. The paper presents methods for the automatic transfer of these anatomical labels to an individual patient data set. The labelled patient data are used to generate 3-D models of the patient's bone structures. Besides the anatomical labelling, the determination of measures, like angles, distances or sizes of contact areas, is important for the planning of hip operations. Thus, algorithms for the automatic computation of orthopaedic parameters were implemented. A first evaluation of the presented atlas-based segmentation method shows a correct labelling of 98.5% of the bony voxels.

Algorithms↗
PubMed2003

Evaluation of a segmentation procedure to delineate organs for use in construction of a radiation therapy planning atlas.

OBJECTIVES: This paper evaluates a semi-automatic segmentation procedure to enhance utilizing atlas based treatment plans. For this application, it is crucial to provide a collection of 'reference' organs, restorable from the atlas so that they closely match those of the current patient. To enable assembling representative organs, we developed a semi-automatic procedure using an active contour method. METHOD: The 3D organ volume was identified by defining contours on individual slices. The initial organ contours were matched to patient volume data sets and then superimposed on them. These starting contours were then adjusted and refined to rapidly find the organ outline of the given patient. Performance was evaluated by contouring organs of different size, shape complexity, and proximity to surrounding structures. We used representative organs defined on CT volumes obtained from 12 patients and compared the resulting outlines to those drawn by a radiologist. RESULTS: A strong correlation was found between the area measures of the delineated liver (r = 0.992), lung (r = 0.996) and spinal cord (r = 0.81), obtained by both segmentation techniques. A paired Student's t-test showed no statistical difference between the two techniques regarding the liver and spinal cord (p > 0.05). CONCLUSION: This method could be used to form 'standard' organs, which would form part of a whole body atlas (WBA) database for radiation treatment plans as well as to match atlas organs to new patient data.

Anatomy, Artistic↗