Cortical Surface Reconstruction from High-Resolution MR Brain Images

Reconstruction of the cerebral cortex from magnetic resonance (MR) images is an important step in quantitative analysis of the human brain structure, for example, in sulcal morphometry and in studies of cortical thickness. Existing cortical reconstruction approaches are typically optimized for standard resolution (~1 mm) data and are not directly applicable to higher resolution images. A new PDE-based method is presented for the automated cortical reconstruction that is computationally efficient and scales well with grid resolution, and thus is particularly suitable for high-resolution MR images with submillimeter voxel size. The method uses a mathematical model of a field in an inhomogeneous dielectric. This field mapping, similarly to a Laplacian mapping, has nice laminar properties in the cortical layer, and helps to identify the unresolved boundaries between cortical banks in narrow sulci. The pial cortical surface is reconstructed by advection along the field gradient as a geometric deformable model constrained by topology-preserving level set approach. The method's performance is illustrated on exvivo images with 0.25–0.35 mm isotropic voxels. The method is further evaluated by cross-comparison with results of the FreeSurfer software on standard resolution data sets from the OASIS database featuring pairs of repeated scans for 20 healthy young subjects

Improvement of source localization by dynamical systems based modelling

Summary: Recently, we have proposed a new concept for analyzing EEG/MEG data (Uhl et al. 1998), which leads to a dynamical systems based modeling (DSBM) of neurophysiological data. We report the application of this approach to four different classes of simulated noisy data sets, to investigate the impact of DSBM-filtering on source localization. An improvement is demonstrated of up to above 50 % of the distance between simulated and estimated dipole positions compared to principal component filtered and unfiltered data. On a noise level on which two underlying dipoles cannot be resolved from the unfiltered data, DSBM allows for an extraction of the two sources

White and Grey Matter Abnormalities in Autism Align with Verbal Ability

This whole-brain structural magnetic resonance imaging (MRI) investigation of autism spectrum disorder (ASD) analyzed white and grey matter concentrations, shape differences, and brain microstructure in 20 adolescents with ASD and 10 neurotypical controls. Evidence for significant group-related differences was found in nine regions, most associated with language processing, including the precentral gyrus, the anterior cingulate, the operculum, superior frontal, and superior temporal gyri. An additional analysis revealed that lower scores from a standardized measure of receptive verbal ability correlated with reduced white matter in the arcuate and uncinate fascicles, inthalamo-frontal and thalamo-cerebellar connections, and in interhemispheric connections passing through the callosal sections I and V. Our findings point to distinct neurological subgroups in ASD which align with the level of verbal ability

A novel maturation index based on neonatal diffusion tensor imaging reflects typical perinatal white matter development in humans

Human birth presents an abrupt transition from intrauterine to extrauterine life. Here we introduce a novel Maturation Index (MI) that considers the relative importance of gestational age at birth and postnatal age at scan in a General Linear Model. The MI is then applied to Diffusion Tensor Imaging (DTI) in newborns for characterizing typical white matter development in neonates. DTI was performed cross-sectionally in 47 neonates (gestational age at birth=39.1±1.6 weeks [GA], postnatal age at scan=25.5±12.2days [SA]). Radial diffusivity (RD), axial diffusivity (AD) and fractional anisotropy (FA) along 27 white matter fiber tracts were considered. The MI was used to characterize inflection in maturation at the time of birth using GLM estimated rates of change before and after birth. It is proposed that the sign (positive versus negative) of MI reflects the period of greatest maturation rate. Two general patterns emerged from the MI analysis. First, RD and AD (but not FA) had positive MI on average across the whole brain (average MIAD=0.31±0.42, average MIRD=0.22±0.34). Second, significant regions of negative MI in RD and FA (but not AD) were observed in the inferior corticospinal regions, areas known to myelinate early. Observations using the proposed method are consistent with proposed models of the white matter maturation process in which pre-myelination is described by changes in AD and RD due to oligodendrocyte proliferation while true myelination is characterized by changes in RD and FA due to myelin formation

Hippocampal Atrophy as a Quantitative Trait in a Genome-Wide Association Study Identifying Novel Susceptibility Genes for Alzheimer's Disease

With the exception of APOE ε4 allele, the common genetic risk factors for sporadic Alzheimer's Disease (AD) are unknown., which can be considered potential “new” candidate loci to explore in the etiology of sporadic AD. These candidates included EFNA5, CAND1, MAGI2, ARSB, and PRUNE2, genes involved in the regulation of protein degradation, apoptosis, neuronal loss and neurodevelopment. Thus, we identified common genetic variants associated with the increased risk of developing AD in the ADNI cohort, and present publicly available genome-wide data. Supportive evidence based on case-control studies and biological plausibility by gene annotation is provided. Currently no available sample with both imaging and genetic data is available for replication.Using hippocampal atrophy as a quantitative phenotype in a genome-wide scan, we have identified candidate risk genes for sporadic Alzheimer's disease that merit further investigation

Slice-to-Volume Nonrigid Registration of Histological Sections to MR Images of the Human Brain.

Registration of histological images to three-dimensional imaging modalities is an important step in quantitative analysis of brain structure, in architectonic mapping of the brain, and in investigation of the pathology of a brain disease. Reconstruction of histology volume from serial sections is a well-established procedure, but it does not address registration of individual slices from sparse sections, which is the aim of the slice-to-volume approach. This study presents a flexible framework for intensity-based slice-to-volume nonrigid registration algorithms with a geometric transformation deformation field parametrized by various classes of spline functions: thin-plate splines (TPS), Gaussian elastic body splines (GEBS), or cubic B-splines. Algorithms are applied to cross-modality registration of histological and magnetic resonance images of the human brain. Registration performance is evaluated across a range of optimization algorithms and intensity-based cost functions. For a particular case of histological data, best results are obtained with a TPS three-dimensional (3D) warp, a new unconstrained optimization algorithm (NEWUOA), and a correlation-coefficient-based cost function

Slice-to-Volume Nonrigid Registration of Histological Sections to MR Images of the Human Brain.

Registration of histological images to three-dimensional imaging modalities is an important step in quantitative analysis of brain structure, in architectonic mapping of the brain, and in investigation of the pathology of a brain disease. Reconstruction of histology volume from serial sections is a well-established procedure, but it does not address registration of individual slices from sparse sections, which is the aim of the slice-to-volume approach. This study presents a flexible framework for intensity-based slice-to-volume nonrigid registration algorithms with a geometric transformation deformation field parametrized by various classes of spline functions: thin-plate splines (TPS), Gaussian elastic body splines (GEBS), or cubic B-splines. Algorithms are applied to cross-modality registration of histological and magnetic resonance images of the human brain. Registration performance is evaluated across a range of optimization algorithms and intensity-based cost functions. For a particular case of histological data, best results are obtained with a TPS three-dimensional (3D) warp, a new unconstrained optimization algorithm (NEWUOA), and a correlation-coefficient-based cost function

Fast Segmentation of Brain Magnetic Resonance

Abstract. We describe a combination of a region growing and a watershed algorithm optimized for the detection of homogeneous structures in magnetic resonance (MR) volume datasets. No prior knowledge is used except a segment model. The adaptation to different data sets is controlled by parameters which can be determined interactively due to the high speed of the algorithm. Results are shown for the segmentation of the basal ganglia and the white matter of the brain.

Abstract Segmentation of MR images with intensity inhomogeneities

A statistical model to segment clinical magnetic resonance (MR) images in the presence of noise and intensity inhomogeneities is proposed. Inhomogeneities are considered to be multiplicative low-frequency variations of intensities that are due to the anomalies of the magnetic fields of the scanners. The measurements are modeled as a Gaussian mixture where inhomogeneities present a bias field in the distributions. The piecewise contiguous nature of the segmentation is modeled by a Markov random field (MRF). A greedy algorithm based on the iterative conditional modes (ICM) algorithm is used to find an optimal segmentation while estimating the model parameters. Results with simulated and hand-segmented images are presented to compare performance of the algorithm with other statistical methods. Seg-mentation results with MR head scans acquired from four different clinical scanners are presented. 0 1998 Elsevier Science B.V