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PubMed2005

The Nuclear Receptor Signaling Atlas: development of a functional atlas of nuclear receptors.

The Nuclear Receptor Signaling Atlas (NURSA) was developed by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), the National Institute on Aging (NIA), and the National Cancer Institute (NCI) of the National Institutes of Health (NIH); the aim of NURSA is to utilize classical approaches to validate existing hypotheses and exploit new and emerging technologies to formulate and test new hypotheses that might elucidate the program of nuclear receptor (NR) structure, function, and role in disease. The means for carrying out this ambitious program required development of interactions among investigators and the combined application of new high-throughput technologies and existing approaches to allow for both mechanistic studies and accrual of large datasets in a discovery-based research effort, all leading to advances with implications for the missions of the NIDDK, NIA, and NCI. A team-based multidisciplinary approach has allowed for both objectives to proceed simultaneously, tied together via a central bioinformatics resource and one web-accessible venue (www.nursa.org). The ultimate goals for the NURSA consortium are to: 1) establish the mechanistic principles of NR function, 2) characterize NR-coregulator complex formation and regulation, 3) map protein-protein interactions for coregulators, 4) identify candidate downstream target genes of NR action, 5) identify target tissue expression of NRs, 6) understand the regulation of NR expression and, 7) integrate existing and emerging information through NURSA bioinformatics tools.

Animals↗
PubMed2006

Generic head models for atlas-based EEG source analysis.

We describe a method for using a generic head model, in the form of an anatomical atlas, to produce EEG source localizations. The atlas is fitted to the subject by a nonrigid warp using a set of surface landmarks. The warped atlas is used to compute a finite element model (FEM) of the forward mapping or lead-fields between neural current generators and the EEG electrodes. These lead-fields are used to localize current sources from the subject's EEG data and the sources are then mapped back to the anatomical atlas. This approach provides a mechanism for comparing source localizations across subjects in an atlas-based coordinate system, which can be used in the large fraction of EEG studies in which MR images are not available. The Montreal brain atlas was used as the reference anatomical atlas and 10 individual MR volumes were used to evaluate the method. The atlas was fitted to each subject's head by a thin-plate-spline (TPS) warp. The spatial locations of a generic 155-electrode configuration were used to constrain the warp. For the purposes of evaluation, dipolar sources were placed on the inner cortical surface in the atlas geometry and transferred to each subject's brain space using a polynomial warp. The parameters of the warp were computed using an intensity-based matching of the atlas and subject brains, thus ensuring that the sources were placed at approximately the same anatomical location in each case. Data were simulated in the subject geometry and a dipole fit was performed on these data using an FEM of the TPS warped atlas. The source positions found in the warped atlas were transferred back to the original atlas and compared to the original position. Sources were simulated at 972 locations evenly distributed over the inner cortical surface of the atlas. The mean error over all 10 subjects was 8.1 mm in the subject space and 15.2 mm in the atlas space. In comparison, using an affine transformation of the electrodes into atlas space and an FEM model generated from the atlas produced mean errors of 22.3 mm in subject space and 19.6 mm in atlas space. With a standard three-shell spherical model the errors were 27.2 mm in the subject space and 34.7 mm when mapped to atlas space.

Brain↗
PubMed2004

Posterior screw placement on the lateral mass of atlas: an anatomic study.

STUDY DESIGN: An anatomic study evaluating the feasibility of posterior screw fixation on the lateral mass of the atlas and comparing the pullout force of C1 posterior lateral mass screws with that of occipital and C2 pedicle screws. OBJECTIVES: To study the feasibility, anatomy, and biomechanics of posterior screw fixation within the lateral mass of the atlas. SUMMARY OF BACKGROUND DATA: Occipitocervical fusion is a common choice for atlantoaxial dislocations. After that the movement of occipitocervical region will be restricted. If screws could be placed in the lateral mass of the atlas, 1) the movement of C0-C1 junction will be preserved; 2) through the screw the dislocated atlas could be pulled backward; and 3) the fractured lateral mass can be fixed using the posterior lateral mass screw directly. METHODS: Thirty atlas specimens of native adults were used to measure pertinent clinical data. Six fresh upper cervical specimens were used to observe the association of the C2 nerve and the lateral mass of the atlas. The pullout force of the C1 lateral mass was measured and compared with that of screws placed into the occiput and C2 pedicle, respectively. RESULTS: The distances from the midline to the midpoint of the C1 lateral mass, to the inner wall of the transverse foramen, and to the inner edge of the pedicle were 17.6 +/- 1.2 mm, 23.0 +/- 1.7 mm, and 14.2 +/-1.1 mm, respectively. The width and height of the C1 lateral mass were 11.6 +/- 1.4 mm and 12.7 +/- 1.0 mm, respectively. The distance between the inferior midpoint of the C1 lateral mass in the transverse plane of the midposterior arch of the atlas to the edge of the inferior atlas joint line was 4.1 +/- 0.7 mm. The width of the posterior arch at the point of vertebral artery overpass was 4.7 +/- 1.0 mm. The observation on the fresh specimens showed that the C2 nerve passes inferolateral to the C1-C2 joint and could be pulled sideways. The screw pullout force within the lateral mass of the atlas was 1818.16 +/- 422.67 N. This is significantly less than that of screws within the occiput, and there was no difference with that of a C2 pedicle screw. CONCLUSION: The width and height of the atlas lateral mass were larger than that of the C2 pedicle, and there was enough space to insert a 3.5-mm diameter screw in the atlas lateral mass over the C2 nerve. The pullout force of the screw on the lateral mass of the atlas was the same as that of the C2 pedicle screw. It is possible toinsert a 3.5-mm screw in the lateral mass of the atlas. The direction of the screw should be about 20 degrees anterosuperior in the vertical plane and 15 degrees inward in the horizontal plane. The suitable length of the screw should be approximately 22 mm inside the lateral mass.

Anthropometry↗
PubMed2003

[Injuries of the atlas].

PURPOSE OF THE STUDY: Injuries of atlas account for 1-2% of all injures of the spine and for 7% of the injuries of the cervical spine. Fractures of atlas occur either as isolated fractures or in combination with the injury of the axis or occipital condyles. The aim of the work is to evaluate a group of patients with the injury of the atlas treated both conservatively and surgically. MATERIAL: Between January 1996 and October 2001 we treated at the Orthopaedic Department of 3rd Medical Faculty, Carles University in Prague 10 patients with the injury of atlas. Between November 2001 and December 2002 we treated at the Orthopaedic Department and Spondylosurgical Department of the Medical Faculty Motol another 5 patients with the injury of atlas. In 10 cases the fracture of atlas was isolated (anterior arch--once, 4 time Jefferson fracture, twice--fracture of massa lateralis), in 5 cases the fracture was associated with the injury of epistropheus (dens type II/posterior arch--twice, dens type II/Jefferson fracture--once, dens type II/massa lateralis--once, hangman fracture type II/posterior atlas arch--once). Teh group of patients included 9 men and 6 women of the average age of 46.6 years (range, 27-85 years). Eight patients were treated conservatively, 7 patients surgically. The most frequent cause of the injury was fall on the head or a severe downward violence in 7 cases, car accident in 4 cases, other causes vere identified in 4 cases. Neurological deficit upon admission was found out only in one patient (Frankel D). METHODS: In isolated injuries of the anterior or posterior arch of atlas we always proceeded conservatively. The cervical spine was fixed for 12 weeks in the Philadelphia collar. One isolated fracture of massa lateralis was also treated conservatively for 12 weeks in the Philadelphia collar. Another case of the same type of fracture was treated surgically by C1-C2 by the Magerl technique supplemented on the intact side by the Gallie wire loop. Two stable Jefferson fractures were treated by the halo vest applied for 12 weeks. Two unstable fractures were handled surgically, once by C1-C2 by the Magerl technique and once by C0-C2 occipitocervical fixation. C1-C2 associated injuries were treated in four cases surgically, three times by a direct dens fixation and once by C1-C2 fixation after Magerl supplemented with the Gallie wire loop. A patient with the associated hangman fracture type II and fracture of the posterior atlas arch refused the surgery and therefore was treated by the halo fixation for 12 weeks. Philadelphia collar was applied to the patients operated on. RESULTS: In the group of the conservatively treated, 3 patients complained of pain in the upper part of cervical spine and head requiring from time to time the administration of analgesics. All fractures healed within 12 weeks and the functional radiographs showed stable C0-C2 segments. As for complications, during the conservative treatment in one case a pyogenic secretion was recorded around the fixation elements of the halo apparatus requiring its removal after 8 weeks. The patient was further treated by a pelot fixation. In one case it was necessary to adjust twice the halo apparatus due to re-dislocation of the hangman fracture (associated hangman fracture of type II and posterior atlas arch). In spite of this the injury healed in C2-C3 subluxation, however, the fracture of atlas healed in a favourable anatomical position. In the group of the operated on, 2 patients complained of pain in the upper cervical spine requiring from time to time the administration of analgesics and one patient complained of a marked limitation of the range of motion by 50% (C0-C2 occipitocervical fixation). Also in this group stable C0-C2 segments were found out 12-14 weeks after the surgery. DISCUSSION: In our group of 15 patients the fracture healed, i.e. stable C0-C1 and C1-C2 segments, in all patients treated both conservatively and surgically. In the group of conservatively treated patients there occurred in one case re-dislocation of the fracture. However, the patient refused the surgery repeatedly. Apart from these case we found in neither group any severe complication. The ratio of conservative and surgical treatment was 8:7. CONCLUSION: Based on our own experience and the literary data we believe that suitable for the treatment of stable injuries of the atlas is conservative treatment, i.e. fixation in the Philadelphia collar for 12 weeks. In unstable injuries or intraarticular injures with dislocation we prefer surgical fixation of C1-C2 or C0-C2 in dependence on the type of injury. All associated injuries are indicated for surgical treatment.

Adult↗
PubMed2000

Development of a logically devised line drawing atlas for grading of knee osteoarthritis.

OBJECTIVES: To (a) develop an atlas of line drawings for the assessment and grading of narrowing and osteophyte (that is, changes of osteoarthritis) on knee radiographs, and (b) compare the performance of this atlas with that of the standard Osteoarthritis Research Society (OARS) photographic atlas of radiographs. METHODS: Normal joint space widths (grade 0) for the medial and lateral tibiofemoral and medial and lateral patellofemoral compartments were obtained from a previous community study. Grades 1-3 narrowing in each compartment was calculated separately for men and women, grade 3 being bone on bone, grades 1 and 2 being two thirds and one third the value of grade 0. Maximum osteophyte size (grade 3) for each of eight sites was determined from 715 bilateral knee x ray films obtained in a knee osteoarthritis (OA) hospital clinic; grades 1-2 were calculated as two thirds and one third reductions in the area of grade 3. Drawings for narrowing and osteophyte were presented separately. 50 sets of bilateral knee x ray radiographs (standing, extended anteroposterior; flexed skyline) showing a spectrum of OA grades were scored by three observers, twice using the OARS atlas and twice using the drawn atlas. RESULTS: Intraobserver and interobserver reproducibility was similar and generally good with both atlases, though varied according to site. All three observers preferred the line drawing atlas for ease and convenience of use. Higher scores for patellofemoral narrowing and lower scores for osteophyte, especially medial femoral osteophyte, were seen using the line drawing atlas, showing that the two atlases are not equivalent instruments. CONCLUSION: A logically derived line drawing atlas for grading of narrowing and osteophyte at the knee has been produced. The atlas showed comparable reproducibility with the OARS atlas, but was discordant in several aspects of grading. Such a system has several theoretical and practical advantages and should be considered for use in knee OA studies.

Adult↗
PubMed2005

Mindboggle: automated brain labeling with multiple atlases.

BACKGROUND: To make inferences about brain structures or activity across multiple individuals, one first needs to determine the structural correspondences across their image data. We have recently developed Mindboggle as a fully automated, feature-matching approach to assign anatomical labels to cortical structures and activity in human brain MRI data. Label assignment is based on structural correspondences between labeled atlases and unlabeled image data, where an atlas consists of a set of labels manually assigned to a single brain image. In the present work, we study the influence of using variable numbers of individual atlases to nonlinearly label human brain image data. METHODS: Each brain image voxel of each of 20 human subjects is assigned a label by each of the remaining 19 atlases using Mindboggle. The most common label is selected and is given a confidence rating based on the number of atlases that assigned that label. The automatically assigned labels for each subject brain are compared with the manual labels for that subject (its atlas). Unlike recent approaches that transform subject data to a labeled, probabilistic atlas space (constructed from a database of atlases), Mindboggle labels a subject by each atlas in a database independently. RESULTS: When Mindboggle labels a human subject's brain image with at least four atlases, the resulting label agreement with coregistered manual labels is significantly higher than when only a single atlas is used. Different numbers of atlases provide significantly higher label agreements for individual brain regions. CONCLUSION: Increasing the number of reference brains used to automatically label a human subject brain improves labeling accuracy with respect to manually assigned labels. Mindboggle software can provide confidence measures for labels based on probabilistic assignment of labels and could be applied to large databases of brain images.

Journal Article↗
PubMed2001

Atlas-assisted localization analysis of functional images.

OBJECTIVE: This paper introduces a method for localization analysis of functional images assisted by a brain atlas. The usefulness of the system developed, based on this method, is analyzed for human brain mapping and neuroradiology. MATERIALS AND METHODS: We use an enhanced and extended electronic Talairach-Tournoux brain atlas, containing segmented and labeled subcortical structures, Brodmann's areas, and gyri. The brain atlas serves as a tool for anatomy referencing, segmentation, labeling, registration, and providing 3D anatomical relationships. The process of localization analysis is decomposed into five steps: data loading, feature extraction, data normalization, identification and editing of loci, and getting labels and values. This analysis is supported by near real-time data-to-atlas warping based on the Talairach transformation. Metanalysis is enabled by merging the current and external lists of activation loci. RESULTS: We have designed, developed, tested, and deployed a commercial system for atlas-assisted localization analysis of functional images. This is the first system where an electronic version of the Talairach-Tournoux brain atlas is used interactively for analysis of functional images. This system runs on personal computers and provides functions for a rapid normalization of anatomical and functional volumetric data, data segmentation and labeling, readout of Talairach coordinates, and data display. It also is empowered with several unique features including: interactive warping facilitating fine tuning of the data-to-atlas fit, a backtracking mechanism to compensate for missing landmarks and enhancing the outcome of the overall process of data analysis, navigation on the triplanar formed by the data and the atlas, multiple-images-in-one display with atlas-anatomy-function blending, a fast locus-controlled generation of results, editing of loci, multiple label display, and saving and reading of loci. The system normalizes a single image in near real-time (0.7 s), so analysis of anatomical and functional datasets can be done on-the-fly regardless of the number of slices. The same task performed by the state-of-the-art non-linear registration methods may require up to several days. CONCLUSIONS: The system is a useful tool for atlas-assisted localization analysis and a helpful adjunct to function/location metanalysis in human brain mapping research. It is also a step forward in bringing the atlas and the clinical data together within a practical and powerful solution that is fast and flexible, yet low-cost and affordable.

Anatomy, Artistic↗
PubMed2005

A Population-Average, Landmark- and Surface-based (PALS) atlas of human cerebral cortex.

This report describes a new electronic atlas of human cerebral cortex that provides a substrate for a wide variety of brain-mapping analyses. The Population-Average, Landmark- and Surface-based (PALS) atlas approach involves surface-based and volume-based representations of cortical shape, each available as population averages and as individual subject data. The specific PALS-B12 atlas introduced here is derived from structural MRI volumes of 12 normal young adults. Accurate cortical surface reconstructions were generated for each hemisphere, and the surfaces were inflated, flattened, and mapped to standard spherical configurations using SureFit and Caret software. A target atlas sphere was generated by averaging selected landmark contours from each of the 24 contributing hemispheres. Each individual hemisphere was deformed to this target using landmark-constrained surface registration. The utility of the resultant PALS-B12 atlas was demonstrated using a variety of analyses. (i) Probabilistic maps of sulcal identity were generated using both surface-based registration (SBR) and conventional volume-based registration (VBR). The SBR approach achieved markedly better consistency of sulcal alignment than did VBR. (ii) A method is introduced for 'multi-fiducial mapping' of volume-averaged group data (e.g., fMRI data, probabilistic architectonic maps) onto each individual hemisphere in the atlas, followed by spatial averaging across the individual maps. This yielded a population-average surface representation that circumvents the biases inherent in choosing any single hemisphere as a target. (iii) Surface-based and volume-based morphometry applied to maps of sulcal depth and sulcal identity demonstrated prominent left-right asymmetries in and near the superior temporal sulcus and Sylvian fissure. Moreover, shape variability in the temporal lobe is significantly greater in the left than the right hemisphere. The PALS-B12 atlas has been registered to other surface-based atlases to facilitate interchange of data and comparison across atlases. All data sets in the PALS-B12 atlas are accessible via the SumsDB database for online and offline visualization and analysis.

Adolescent↗
PubMed2006

A hybrid approach to shape-based interpolation of stereotactic atlases of the human brain.

Stereotactic human brain atlases, either in print or electronic form, are useful not only in functional neurosurgery, but also in neuroradiology, human brain mapping, and neuroscience education. The existing atlases represent structures on 2D plates taken at variable, often large intervals, which limit their applications. To overcome this problem, we propose a hybrid interpolation approach to build high-resolution brain atlases from the existing ones. In this approach, all section regions of each object are grouped into two types of components: simple and complex. A NURBS-based method is designed for interpolation of the simple components, and a distance map-based method for the complex components. Once all individual objects in the atlas are interpolated, the results are combined hierarchically in a bottom-up manner to produce the interpolation of the entire atlas. In the procedure, different knowledge-based and heuristic strategies are used to preserve various topological relationships. The proposed approach has been validated quantitatively and used for interpolation of two stereotactic brain atlases: the Talairach-Tournoux atlas and Schaltenbrand-Wahren atlas. The interpolations produced are of high resolution and feature high accuracy, 3D consistency, smooth surface, and preserved topology. They potentially open new applications for electronic stereotactic brain atlases, such as atlas reformatting, accurate 3D display, and 3D nonlinear warping against normal and pathological scans. The proposed approach is also potentially useful in other applications, which require interpolation and 3D modeling from sparse and/or variable intersection interval data. An example of 3D modeling of an infarct from MR diffusion images is presented.

Algorithms↗
PubMed1998

Microelectrode-guided functional neurosurgery assisted by Electronic Clinical Brain Atlas CD-ROM.

The Electronic Clinical Brain Atlas is a CD-ROM containing several classic brain atlases and a real-time yet simple registration function that deforms the atlases to match them with specific patient studies. This article presents the use of this registration function for functional neurosurgery planning. We first propose the CD-ROM assisted planning procedure, then illustrate it with two cases: a pallidal stimulation and a thalamic stimulation. The Schaltenbrand-Wahren atlas is registered and scaled to conform with an actual patient's data by means of two-dimensional (2-D) local deformations performed in multiple orientations. First a rectangular region of interest (ROI), which is set between any clearly visible landmarks chosen by the neurosurgeon, is measured on the film or scanner console. The corresponding atlas plate with the target is then deformed in real time for the same landmarks, such that the dimensions of this ROI are the same on the film and on the deformed atlas plate. Next the target is set on the deformed (individualized) atlas plate and its coordinates are read. The individualized atlas plate can also be printed on transparent foil and superimposed on the film or, alternatively, this superimposition can be done electronically. The planning steps can be repeated for all available orientations. The proposed atlas-assisted planning procedure extends the traditional use of printed stereotactic atlases by individualizing them to specific patients. The preliminary results show that this procedure may improve the definition of the target and may have several advantages over other approaches, such as indirect measurements based on the AC-PC line or 1-D (intercommissural distance based) scaling. It provides the neurosurgeon with a convenient and immediate means of accessing ancillary data that is usually only available in the printed form.

Anatomy, Artistic↗
PubMed2004

A unified approach for morphometric and functional data analysis in young, old, and demented adults using automated atlas-based head size normalization: reliability and validation against manual measurement of total intracranial volume.

Atlas normalization, as commonly used by functional data analysis, provides an automated solution to the widely encountered problem of correcting for head size variation in regional and whole-brain morphometric analyses, so long as an age- and population-appropriate target atlas is used. In the present article, we develop and validate an atlas normalization procedure for head size correction using manual total intracranial volume (TIV) measurement as a reference. The target image used for atlas transformation consisted of a merged young and old-adult template specifically created for cross age-span normalization. Automated atlas transformation generated the Atlas Scaling Factor (ASF) defined as the volume-scaling factor required to match each individual to the atlas target. Because atlas normalization equates head size, the ASF should be proportional to TIV. A validation analysis was performed on 147 subjects to evaluate ASF as a proxy for manual TIV measurement. In addition, 19 subjects were imaged on multiple days to assess test-retest reliability. Results indicated that the ASF was (1) equivalent to manual TIV normalization (r = 0.93), (2) reliable across multiple imaging sessions (r = 1.00; mean absolute percentage of difference = 0.51%), (3) able to connect between-gender head size differences, and (4) minimally biased in demented older adults with marked atrophy. Hippocampal volume differences between nondemented (n = 49) and demented (n = 50) older adults (measured manually) were equivalent whether corrected using manual TIV or automated ASF (effect sizes of 1.29 and 1.46, respectively). To provide normative values, ASF was used to automatically derive estimated TIV (eTIV) in 335 subjects aged 15-96 including both clinically characterized nondemented (n = 77) and demented (n = 90) older adults. Differences in eTIV between nondemented and demented groups were negligible, thus failing to support the hypothesis that large premorbid brain size moderates Alzheimer's disease. Gender was the only robust factor that influenced eTIV. Men showed an approximately approximately 12% larger eTIV than women. These results demonstrate that atlas normalization using appropriate template images provides a robust, automated method for head size correction that is equivalent to manual TIV correction in studies of aging and dementia. Thus, atlas normalization provides a common framework for both morphometric and functional data analysis.

Adolescent↗
PubMedDate not supplied

Digital hand atlas and web-based bone age assessment: system design and implementation.

Bone age assessment is a procedure frequently performed in pediatric patients to evaluate their growth disorder. A simple method commonly used in bone age assessment is atlas matching by a radiological examination of a left-hand radiograph against a small reference set of Greulich-Pyle atlas patterns of normal standards. The method however can lead to significant deviation in age assessment, due to a variety of observers with different levels of training. The Greulich-Pyle atlas developed in the 1950s based on middle upper class white populations, is also not fully applicable for children of today, especially regarding the standard development in other racial groups. In this paper, we present our system design and initial implementation of a digital hand atlas and computer-aided diagnostic (CAD) system for Web-based bone age assessment. The CAD system is built on top of existing picture archiving and communication system (PACS), as well as recent advances in Internet technology. It consists of a hand atlas database, a CAD module and a Java-based Web user interface. The digital atlas is based on a large new set of clinically normal hand images of diverse ethnic groups. A relational image database system is used to organize hand images, their extracted quantitative features and patient data. The digital atlas removes the disadvantages of the currently out-of-date Greulich-Pyle atlas and allows the bone age assessment to be computerized. The Java-based Web user interface allows users to interact with the hand image database from browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, are then extracted and compared with patterns from the atlas database to assess the bone age. The digital atlas method based on open system Internet technology provides an alternative to supplement or replace the traditional one for a quantitative, accurate and cost-effective assessment of bone age.

Adolescent↗