Robust estimation of group-wise cortical correspondence with an application to macaque and human neuroimaging studies.

We present a novel group-wise registration method for cortical correspondence for local cortical thickness analysis in human and non-human primate neuroimaging studies. The proposed method is based on our earlier template based registration that estimates a continuous, smooth deformation field via sulcal curve-constrained registration employing spherical harmonic decomposition of the deformation field. This pairwise registration though results in a well-known template selection bias, which we aim to overcome here via a group-wise approach.

Automatic Tissue Segmentation of Neonate Brain MR Images with Subject-specific Atlases.

Automatic tissue segmentation of the neonate brain using Magnetic Resonance Images (MRI) is extremely important to study brain development and perform early diagnostics but is challenging due to high variability and inhomogeneity in contrast throughout the image due to incomplete myelination of the white matter tracts. For these reasons, current methods often totally fail or give unsatisfying results. Furthermore, most of the subcortical midbrain structures are misclassified due to a lack of contrast in these regions.

Osteocyte specific responses to soluble and mechanical stimuli in a stem cell derived culture model.

Studying osteocyte behavior in culture has proven difficult because these embedded cells require spatially coordinated interactions with the matrix and surrounding cells to achieve the osteocyte phenotype. Using an easily attainable source of bone marrow mesenchymal stem cells, we generated cells with the osteocyte phenotype within two weeks. These "stem cell derived-osteocytes" (SCD-O) displayed stellate morphology and lacunocanalicular ultrastructure.

Evaluation of machine learning algorithms for treatment outcome prediction in patients with epilepsy based on structural connectome data.

The objective of this study is to evaluate machine learning algorithms aimed at predicting surgical treatment outcomes in groups of patients with temporal lobe epilepsy (TLE) using only the structural brain connectome. Specifically, the brain connectome is reconstructed using white matter fiber tracts from presurgical diffusion tensor imaging. To achieve our objective, a two-stage connectome-based prediction framework is developed that gradually selects a small number of abnormal network connections that contribute to the surgical treatment outcome, and in each stage a linear kernel operation is used to further improve the accuracy of the learned classifier.

Exercise Regulation of Marrow Fat in the Setting of PPARγ Agonist Treatment in Female C57BL/6 Mice.

The contribution of marrow adipose tissue (MAT) to skeletal fragility is poorly understood. Peroxisome proliferator-activated receptor (PPAR)γ agonists, associated with increased fractures in diabetic patients, increase MAT. Here, we asked whether exercise could limit the MAT accrual and increase bone formation in the setting of PPARγ agonist treatment.

A diffusion tensor MRI atlas of the postmortem rhesus macaque brain.

The rhesus macaque (Macaca mulatta) is the most widely used nonhuman primate for modeling the structure and function of the brain. Brain atlases, and particularly those based on magnetic resonance imaging (MRI), have become important tools for understanding normal brain structure, and for identifying structural abnormalities resulting from disease states, exposures, and/or aging. Diffusion tensor imaging (DTI)-based MRI brain atlases are widely used in both human and macaque brain imaging studies because of the unique contrasts, quantitative diffusion metrics, and diffusion tractography that they can provide.

Skeletal shape correspondence via entropy minimization.

Purpose: Improving the shape statistics of medical image objects by generating correspondence of interior skeletal points.

Data: Synthetic objects and real world lateral ventricles segmented from MR images.

Methods: Each object's interior is modeled by a skeletal representation called the s-rep, which is a quadrilaterally sampled, folded 2-sided skeletal sheet with spoke vectors proceeding from the sheet to the boundary.

Shape index distribution based local surface complexity applied to the human cortex.

The quantification of local surface complexity in the human cortex has shown to be of interest in investigating population differences as well as developmental changes in neurodegenerative or neurodevelopment diseases. We propose a novel assessment method that represents local complexity as the difference between the observed distributions of local surface topology to its best-fit basic topology model within a given local neighborhood. This distribution difference is estimated via Earth Move Distance (EMD) over the histogram within the local neighborhood of the surface topology quantified via the Shape Index (SI) measure.

LOGISMOS-B for Primates: Primate Cortical Surface Reconstruction and Thickness Measurement.

Cortical thickness and surface area are important morphological measures with implications for many psychiatric and neurological conditions. Automated segmentation and reconstruction of the cortical surface from 3D MRI scans is challenging due to the variable anatomy of the cortex and its highly complex geometry. While many methods exist for this task in the context of the human brain, these methods are typically not readily applicable to the primate brain.

Automatic Sulcal Curve Extraction on the Human Cortical Surface.

The recognition of sulcal regions on the cortical surface is an important task to shape analysis and landmark detection. However, it is challenging especially in a complex, rough human cortex. In this paper, we focus on the extraction of sulcal curves from the human cortical surface.

Altered corpus callosum morphology associated with autism over the first 2 years of life.

Numerous brain imaging studies indicate that the corpus callosum is smaller in older children and adults with autism spectrum disorder. However, there are no published studies examining the morphological development of this connective pathway in infants at-risk for the disorder. Magnetic resonance imaging data were collected from 270 infants at high familial risk for autism spectrum disorder and 108 low-risk controls at 6, 12 and 24 months of age, with 83% of infants contributing two or more data points.

Incorporating 3-dimensional models in online articles.

Introduction: The aims of this article are to introduce the capability to view and interact with 3-dimensional (3D) surface models in online publications, and to describe how to prepare surface models for such online 3D visualizations.

Methods: Three-dimensional image analysis methods include image acquisition, construction of surface models, registration in a common coordinate system, visualization of overlays, and quantification of changes. Cone-beam computed tomography scans were acquired as volumetric images that can be visualized as 3D projected images or used to construct polygonal meshes or surfaces of specific anatomic structures of interest.

3D superimposition and understanding temporomandibular joint arthritis.

Objectives: To investigate the 3D morphological variations in 169 temporomandibular ioint (TMJ) condyles, using novel imaging statistical modeling approaches.

Setting And Sample Population: The Department of Orthodontics and Pediatric Dentistry at the University of Michigan. Cone beam CT scans were acquired from 69 subjects with long-term TMJ osteoarthritis (OA, mean age 39.

Regional differences in fiber tractography predict neurodevelopmental outcomes in neonates with infantile Krabbe disease.

Background: Krabbe disease is a fatal neurodegenerative disease caused by rapid demyelination of the central and peripheral nervous systems. The only available treatment, unrelated umbilical cord blood transplantation, is effective only if performed before clinical symptoms appear. Phenotypic expressions of disease-causing mutations vary widely, but genotype-phenotype relationships are unclear.

Cell Mechanosensitivity to Extremely Low-Magnitude Signals Is Enabled by a LINCed Nucleus.

A cell's ability to recognize and adapt to the physical environment is central to its survival and function, but how mechanical cues are perceived and transduced into intracellular signals remains unclear. In mesenchymal stem cells (MSCs), high-magnitude substrate strain (HMS, ≥2%) effectively suppresses adipogenesis via induction of focal adhesion (FA) kinase (FAK)/mTORC2/Akt signaling generated at FAs. Physiologic systems also rely on a persistent barrage of low-level signals to regulate behavior.

Accurate age classification of 6 and 12 month-old infants based on resting-state functional connectivity magnetic resonance imaging data.

Human large-scale functional brain networks are hypothesized to undergo significant changes over development. Little is known about these functional architectural changes, particularly during the second half of the first year of life. We used multivariate pattern classification of resting-state functional connectivity magnetic resonance imaging (fcMRI) data obtained in an on-going, multi-site, longitudinal study of brain and behavioral development to explore whether fcMRI data contained information sufficient to classify infant age.

Quantitative tract-based white matter heritability in twin neonates.

Studies in adults indicate that white matter microstructure, assessed with diffusion tensor imaging (DTI), has high heritability. Little is known about genetic and environmental influences on DTI parameters, measured along fiber tracts particularly, in early childhood. In the present study, we report comprehensive heritability data of white matter microstructure fractional anisotropy (FA), radial diffusion (RD), and axial diffusion (AD) along 47 fiber tracts using the quantitative tractography in a large sample of neonatal twins (n=356).

Subject-Motion Correction in HARDI Acquisitions: Choices and Consequences.

Diffusion-weighted imaging (DWI) is known to be prone to artifacts related to motion originating from subject movement, cardiac pulsation, and breathing, but also to mechanical issues such as table vibrations. Given the necessity for rigorous quality control and motion correction, users are often left to use simple heuristics to select correction schemes, which involves simple qualitative viewing of the set of DWI data, or the selection of transformation parameter thresholds for detection of motion outliers. The scientific community offers strong theoretical and experimental work on noise reduction and orientation distribution function (ODF) reconstruction techniques for HARDI data, where post-acquisition motion correction is widely performed, e.

Effects of prenatal cocaine exposure on early postnatal rodent brain structure and diffusion properties.

Prenatal cocaine exposure has been associated with numerous behavioral phenotypes in clinical populations, including impulsivity, reduced attention, alterations in social behaviors, and delayed language and sensory-motor development. Detecting associated changes in brain structure in these populations has proven difficult, and results have been inconclusive and inconsistent. Due to their more controlled designs, animal models may shed light on the neuroanatomical changes caused by prenatal cocaine; however, to maximize clinical relevance, data must be carefully collected using translational methods.

A JOINT FRAMEWORK FOR 4D SEGMENTATION AND ESTIMATION OF SMOOTH TEMPORAL APPEARANCE CHANGES.

Medical imaging studies increasingly use longitudinal images of individual subjects in order to follow-up changes due to development, degeneration, disease progression or efficacy of therapeutic intervention. Repeated image data of individuals are highly correlated, and the strong causality of information over time lead to the development of procedures for joint segmentation of the series of scans, called 4D segmentation. A main aim was improved consistency of quantitative analysis, most often solved via patient-specific atlases.

A PRELIMINARY STUDY ON THE EFFECT OF MOTION CORRECTION ON HARDI RECONSTRUCTION.

Post-acquisition motion correction is widely performed in diffusion-weighted imaging (DWI) to guarantee voxel-wise correspondence between DWIs. Whereas this is primarily motivated to save as many scans as possible if corrupted by motion, users do not fully understand the consequences of different types of interpolation schemes on the final analysis. Nonetheless, interpolation might increase the partial volume effect while not preserving the volume of the diffusion profile, whereas excluding poor DWIs may affect the ability to resolve crossing fibers especially with small separation angles.

PARAMETRIC REGRESSION SCHEME FOR DISTRIBUTIONS: ANALYSIS OF DTI FIBER TRACT DIFFUSION CHANGES IN EARLY BRAIN DEVELOPMENT.

Temporal modeling frameworks often operate on scalar variables by summarizing data at initial stages as statistical summaries of the underlying distributions. For instance, DTI analysis often employs summary statistics, like mean, for regions of interest and properties along fiber tracts for population studies and hypothesis testing. This reduction via discarding of variability information may introduce significant errors which propagate through the procedures.

Separability tests for high-dimensional, low sample size multivariate repeated measures data.

Longitudinal imaging studies have moved to the forefront of medical research due to their ability to characterize spatio-temporal features of biological structures across the lifespan. Valid inference in longitudinal imaging requires enough flexibility of the covariance model to allow reasonable fidelity to the true pattern. On the other hand, the existence of computable estimates demands a parsimonious parameterization of the covariance structure.

3D osteoarthritic changes in TMJ condylar morphology correlates with specific systemic and local biomarkers of disease.

Objective: To assess 3D morphological variations and local and systemic biomarker profiles in subjects with a diagnosis of temporomandibular joint osteoarthritis (TMJ OA).

Design: Twenty-eight patients with long-term TMJ OA (39.9 ± 16 years), 12 patients at initial diagnosis of OA (47.

Multivariate longitudinal shape analysis of human lateral ventricles during the first twenty-four months of life.

Background: Little is known about the temporospatial shape characteristics of human lateral ventricles (LVs) during the first two years of life. This study aimed to delineate the morphological growth characteristics of LVs during early infancy using longitudinally acquired MR images in normal healthy infants.

Methods: 24 healthy infants were MR imaged starting from 2 weeks old every 3 months during the first and every 6 months during the second year.