A fully segmented 3D anatomical atlas of a lizard brain.

As the relevance of lizards in evolutionary neuroscience increases, so does the need for more accurate anatomical references. Moreover, the use of magnetic resonance imaging (MRI) in evolutionary neuroscience is becoming more widespread; this represents a fundamental methodological shift that opens new avenues of investigative possibility but also poses new challenges. Here, we aim to facilitate this shift by providing a three-dimensional segmentation atlas of the tawny dragon brain.

A 3D MRI-based atlas of a lizard brain.

Magnetic resonance imaging (MRI) is an established technique for neuroanatomical analysis, being particularly useful in the medical sciences. However, the application of MRI to evolutionary neuroscience is still in its infancy. Few magnetic resonance brain atlases exist outside the standard model organisms in neuroscience and no magnetic resonance atlas has been produced for any reptile brain.

Whole-Volume Clustering of Time Series Data from Zebrafish Brain Calcium Images via Mixture Modeling.

Calcium is a ubiquitous messenger in neural signaling events. An increasing number of techniques are enabling visualization of neurological activity in animal models via luminescent proteins that bind to calcium ions. These techniques generate large volumes of spatially correlated time series.

The Study of Neurocognitive Outcomes, Radiological and Retinal Effects of Aspirin in Sleep Apnoea- rationale and methodology of the SNORE-ASA study.

Purpose: Sleep disordered breathing (SDB) is highly prevalent in older adults. Increasing evidence links SDB to the risk of dementia, mediated via a number of pathways, some of which may be attenuated by low-dose aspirin. This study will evaluate, in a healthy older cohort, the prospective relationship between SDB and cognitive function, changes in retinal and cerebral microvasculature, and determine whether low-dose aspirin ameliorates the effects of SDB on these outcomes over 3years.

Evidence for Concerted and Mosaic Brain Evolution in Dragon Lizards.

The brain plays a critical role in a wide variety of functions including behaviour, perception, motor control, and homeostatic maintenance. Each function can undergo different selective pressures over the course of evolution, and as selection acts on the outputs of brain function, it necessarily alters the structure of the brain. Two models have been proposed to explain the evolutionary patterns observed in brain morphology.

An ontologically consistent MRI-based atlas of the mouse diencephalon.

In topological terms, the diencephalon lies between the hypothalamus and the midbrain. It is made up of three segments, prosomere 1 (pretectum), prosomere 2 (thalamus), and prosomere 3 (the prethalamus). A number of MRI-based atlases of different parts of the mouse brain have already been published, but none of them displays the segments the diencephalon and their component nuclei.

Maximum Pseudolikelihood Estimation for Model-Based Clustering of Time Series Data.

Mixture of autoregressions (MoAR) models provide a model-based approach to the clustering of time series data. The maximum likelihood (ML) estimation of MoAR models requires evaluating products of large numbers of densities of normal random variables. In practical scenarios, these products converge to zero as the length of the time series increases, and thus the ML estimation of MoAR models becomes infeasible without the use of numerical tricks.

MINC 2.0: A Flexible Format for Multi-Modal Images.

It is often useful that an imaging data format can afford rich metadata, be flexible, scale to very large file sizes, support multi-modal data, and have strong inbuilt mechanisms for data provenance. Beginning in 1992, MINC was developed as a system for flexible, self-documenting representation of neuroscientific imaging data with arbitrary orientation and dimensionality. The MINC system incorporates three broad components: a file format specification, a programming library, and a growing set of tools.

Robust methods to create ex vivo minimum deformation atlases for brain mapping.

Highly detailed ex vivo 3D atlases of average structure are of critical importance to neuroscience and its current push to understanding the global microstructure of the brain. Multiple single slice histology sections can no longer provide sufficient detail of inter-slice microstructure and lack out of plane resolution. Two ex vivo methods have emerged that can create such detailed models.

Development of MRI-based atlases of non-human brains.

Brain atlases are a fundamental resource for neuroscience research. In the past few decades they have undergone a transition from traditional printed histological atlases to digital atlases made up of multiple data sets from multiple modalities, and atlases based on magnetic resonance imaging (MRI) have become widespread. Here we discuss the methods involved in making an MRI brain atlas, including registration of multiple data sets into a model, ontological classification, segmentation of a minimum deformation model, dissemination strategies, and applications of these atlases.

Relating education, brain structure, and cognition: the role of cardiovascular disease risk factors.

The protective effect of education on cognitive and brain health is well established. While the direct effects of individual cardiovascular disease (CVD) risk factors (i.e.

Blood pressure, brain structure, and cognition: opposite associations in men and women.

Background: Research on associations between blood pressure, brain structure, and cognitive function has produced somewhat inconsistent results. In part, this may be due to differences in age ranges studied and because of sex differences in physiology and/or exposure to risk factors, which may lead to different time course or patterns in cardiovascular disease progression. The aim of this study was to investigate the impact of sex on associations between blood pressure, regional cerebral volumes, and cognitive function in older individuals.

False discovery rate control in magnetic resonance imaging studies via Markov random fields.

Magnetic resonance imaging (MRI) is widely used to study population effects of factors on brain morphometry. Inference from such studies often require the simultaneous testing of millions of statistical hypotheses. Such scale of inference is known to lead to large numbers of false positive results.

High "normal" blood glucose is associated with decreased brain volume and cognitive performance in the 60s: the PATH through life study.

Context: Type 2 diabetes is associated with cerebral atrophy, cognitive impairment and dementia. We recently showed higher glucose levels in the normal range not to be free of adverse effects and to be associated with greater hippocampal and amygdalar atrophy in older community-dwelling individuals free of diabetes.

Objective: This study aimed to determine whether blood glucose levels in the normal range (<6.

Interpretation of medical imaging data with a mobile application: a mobile digital imaging processing environment.

Digital Imaging Processing (DIP) requires data extraction and output from a visualization tool to be consistent. Data handling and transmission between the server and a user is a systematic process in service interpretation. The use of integrated medical services for management and viewing of imaging data in combination with a mobile visualization tool can be greatly facilitated by data analysis and interpretation.

Heterozygosity for nuclear factor one x affects hippocampal-dependent behaviour in mice.

Identification of the genes that regulate the development and subsequent functioning of the hippocampus is pivotal to understanding the role of this cortical structure in learning and memory. One group of genes that has been shown to be critical for the early development of the hippocampus is the Nuclear factor one (Nfi) family, which encodes four site-specific transcription factors, NFIA, NFIB, NFIC and NFIX. In mice lacking Nfia, Nfib or Nfix, aspects of early hippocampal development, including neurogenesis within the dentate gyrus, are delayed.

An MRI atlas of the mouse basal ganglia.

The basal ganglia are a group of subpallial nuclei that play an important role in motor, emotional, and cognitive functions. Morphological changes and disrupted afferent/efferent connections in the basal ganglia have been associated with a variety of neurological disorders including psychiatric and movement disorders. While high-resolution magnetic resonance imaging has been used to characterize changes in brain structure in mouse models of these disorders, no systematic method for segmentation of the C57BL/6 J mouse basal ganglia exists.

A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex.

The neocortex is the largest component of the mammalian cerebral cortex. It integrates sensory inputs with experiences and memory to produce sophisticated responses to an organism's internal and external environment. While areal patterning of the mouse neocortex has been mapped using histological techniques, the neocortex has not been comprehensively segmented in magnetic resonance images.

Segmentation of the C57BL/6J mouse cerebellum in magnetic resonance images.

The C57BL mouse is the centerpiece of efforts to use gene-targeting technology to understand cerebellar pathology, thus creating a need for a detailed magnetic resonance imaging (MRI) atlas of the cerebellum of this strain. In this study we present a methodology for systematic delineation of the vermal and hemispheric lobules of the C57BL/6J mouse cerebellum in magnetic resonance images. We have successfully delineated 38 cerebellar and cerebellar-related structures.

Brain templates and atlases.

The core concept within the field of brain mapping is the use of a standardized, or "stereotaxic", 3D coordinate frame for data analysis and reporting of findings from neuroimaging experiments. This simple construct allows brain researchers to combine data from many subjects such that group-averaged signals, be they structural or functional, can be detected above the background noise that would swamp subtle signals from any single subject. Where the signal is robust enough to be detected in individuals, it allows for the exploration of inter-individual variance in the location of that signal.

New prototype neuronavigation system based on preoperative imaging and intraoperative freehand ultrasound: system description and validation.

Purpose: The aim of this report is to present IBIS (Interactive Brain Imaging System) NeuroNav, a new prototype neuronavigation system that has been developed in our research laboratory over the past decade that uses tracked intraoperative ultrasound to address surgical navigation issues related to brain shift. The unique feature of the system is its ability, when needed, to improve the initial patient-to-preoperative image alignment based on the intraoperative ultrasound data. Parts of IBIS Neuronav source code are now publicly available on-line.

Cerebral white matter in early puberty is associated with luteinizing hormone concentrations.

Puberty is a period in which cerebral white matter grows considerably, whereas gray matter decreases. The first endocrinological marker of puberty in both boys and girls is an increased secretion of luteinizing hormone (LH). Here we investigated the phenotypic association between LH, global and focal gray and white matter in 104 healthy nine-year-old monozygotic and dizygotic twins.

Intensity non-uniformity correction using N3 on 3-T scanners with multichannel phased array coils.

Measures of structural brain change based on longitudinal MR imaging are increasingly important but can be degraded by intensity non-uniformity. This non-uniformity can be more pronounced at higher field strengths, or when using multichannel receiver coils. We assessed the ability of the non-parametric non-uniform intensity normalization (N3) technique to correct non-uniformity in 72 volumetric brain MR scans from the preparatory phase of the Alzheimer's Disease Neuroimaging Initiative (ADNI).

Gray and white matter changes in Alzheimer's disease: a diffusion tensor imaging study.

Purpose: To investigate microstructural changes in cortical and white matter pathways in patients with Alzheimer's disease using diffusion tensor imaging (DTI).

Materials And Methods: Measures of mean diffusivity (MD) and fractional anisotropy (FA) were compared in the brains of 13 Alzheimer's disease (AD) patients and a group of 13 aged-matched control participants employing an optimized DTI technique involving a fully automated, voxel-based morphometric (VBM) analysis.

Results: After rigorous control for anatomical variation and confounding partial volume effects, we found significantly elevated MD measures within the hippocampus, amygdala, and medial temporal, parietal, and frontal lobe gray matter regions in the AD participants.

Symmetric atlasing and model based segmentation: an application to the hippocampus in older adults.

In model-based segmentation, automated region identification is achieved via registration of novel data to a pre-determined model. The desired structure is typically generated via manual tracing within this model. When model-based segmentation is applied to human cortical data, problems arise if left-right comparisons are desired.