Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Corticospinal Tract (CST) reconstruction based on fiber orientation distributions(FODs) tractography

The Corticospinal Tract (CST) is a part of pyramidal tract (PT), and it can innervate the voluntary movement of skeletal muscle through spinal interneurons (the 4th layer of the Rexed gray board layers), and anterior horn motorneurons (which control trunk and proximal limb muscles). Spinal cord injury (SCI) is a highly disabling disease often caused by traffic accidents. The recovery of CST and the functional reconstruction of spinal anterior horn motor neurons play an essential role in the treatment of SCI. However, the localization and reconstruction of CST are still challenging issues; the accuracy of the geometric reconstruction can directly affect the results of the surgery. The main contribution of this paper is the reconstruction of the CST based on the fiber orientation distributions (FODs) tractography. Differing from tensor-based tractography in which the primary direction is a determined orientation, the direction of FODs tractography is determined by the probability. The spherical harmonics (SPHARM) can be used to approximate the efficiency of FODs tractography. We manually delineate the three ROIs (the posterior limb of the internal capsule, the cerebral peduncle, and the anterior pontine area) by the ITK-SNAP software, and use the pipeline software to reconstruct both the left and right sides of the CST fibers. Our results demonstrate that FOD-based tractography can show more and correct anatomical CST fiber bundles

Intersubject Regularity in the Intrinsic Shape of Human V1

Previous studies have reported considerable intersubject variability in the three-dimensional geometry of the human primary visual cortex (V1). Here we demonstrate that much of this variability is due to extrinsic geometric features of the cortical folds, and that the intrinsic shape of V1 is similar across individuals. V1 was imaged in ten ex vivo human hemispheres using high-resolution (200 μm) structural magnetic resonance imaging at high field strength (7 T). Manual tracings of the stria of Gennari were used to construct a surface representation, which was computationally flattened into the plane with minimal metric distortion. The instrinsic shape of V1 was determined from the boundary of the planar representation of the stria. An ellipse provided a simple parametric shape model that was a good approximation to the boundary of flattened V1. The aspect ration of the best-fitting ellipse was found to be consistent across subject, with a mean of 1.85 and standard deviation of 0.12. Optimal rigid alignment of size-normalized V1 produced greater overlap than that achieved by previous studies using different registration methods. A shape analysis of published macaque data indicated that the intrinsic shape of macaque V1 is also stereotyped, and similar to the human V1 shape. Previoud measurements of the functional boundary of V1 in human and macaque are in close agreement with these results

Mapping the human cortical surface by combining quantitative T(1) with retinotopy

We combined quantitative relaxation rate (R1= 1/T1) mapping-to measure local myelination-with fMRI-based retinotopy. Gray-white and pial surfaces were reconstructed and used to sample R1 at different cortical depths. Like myelination, R1 decreased from deeper to superficial layers. R1 decreased passing from V1 and MT, to immediately surrounding areas, then to the angular gyrus. High R1 was correlated across the cortex with convex local curvature so the data was first "de-curved". By overlaying R1 and retinotopic maps, we found that many visual area borders were associated with significant R1 increases including V1, V3A, MT, V6, V6A, V8/VO1, FST, and VIP. Surprisingly, retinotopic MT occupied only the posterior portion of an oval-shaped lateral occipital R1 maximum. R1 maps were reproducible within individuals and comparable between subjects without intensity normalization, enabling multi-center studies of development, aging, and disease progression, and structure/function mapping in other modalities

Imaging Informatics and the Human Brain Project: the Role of Structure, Review

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Structure and stimulus familiarity: A study of memory in chess-players with functional magnetic resonance imaging.

A grandmaster and an international chess master were compared with a group of novices in a memory task with chess and non-chess stimuli, varying the structure and familiarity of the stimuli, while functional magnetic resonance images were acquired. The pattern of brain activity in the masters was different from that of the novices. Masters showed no differences in brain activity when different degrees of structure and familiarity where compared; however, novices did show differences in brain activity in such contrasts. The most important differences were found in the contrast of stimulus familiarity with chess positions. In this contrast, there was an extended brain activity in bilateral frontal areas such as the anterior cingulate and the superior, middle, and inferior frontal gyri; furthermore, posterior areas, such as posterior cingulate and cerebellum, showed great bilateral activation. These results strengthen the hypothesis that when performing a domain-specific task, experts activate different brain systems from that of novices. The use of the expertsversus- novices paradigm in brain imaging contributes towards the search for brain systems involved in cognitive processes

Adolescent brain maturation and cortical folding: evidence for reductions in gyrification

Evidence from anatomical and functional imaging studies have highlighted major modifications of cortical circuits during adolescence. These include reductions of gray matter (GM), increases in the myelination of cortico-cortical connections and changes in the architecture of large-scale cortical networks. It is currently unclear, however, how the ongoing developmental processes impact upon the folding of the cerebral cortex and how changes in gyrification relate to maturation of GM/WM-volume, thickness and surface area. In the current study, we acquired high-resolution (3 Tesla) magnetic resonance imaging (MRI) data from 79 healthy subjects (34 males and 45 females) between the ages of 12 and 23 years and performed whole brain analysis of cortical folding patterns with the gyrification index (GI). In addition to GI-values, we obtained estimates of cortical thickness, surface area, GM and white matter (WM) volume which permitted correlations with changes in gyrification. Our data show pronounced and widespread reductions in GI-values during adolescence in several cortical regions which include precentral, temporal and frontal areas. Decreases in gyrification overlap only partially with changes in the thickness, volume and surface of GM and were characterized overall by a linear developmental trajectory. Our data suggest that the observed reductions in GI-values represent an additional, important modification of the cerebral cortex during late brain maturation which may be related to cognitive development