Development of an Atlas-Based Segmentation of Cranial Nerves Using Shape-Aware Discrete Deformable Models for Neurosurgical Planning and Simulation

Twelve pairs of cranial nerves arise from the brain or brainstem and control our sensory functions such as vision, hearing, smell and taste as well as several motor functions to the head and neck including facial expressions and eye movement. Often, these cranial nerves are difficult to detect in MRI data, and thus represent problems in neurosurgery planning and simulation, due to their thin anatomical structure, in the face of low imaging resolution as well as image artifacts. As a result, they may be at risk in neurosurgical procedures around the skull base, which might have dire consequences such as the loss of eyesight or hearing and facial paralysis. Consequently, it is of great importance to clearly delineate cranial nerves in medical images for avoidance in the planning of neurosurgical procedures and for targeting in the treatment of cranial nerve disorders. In this research, we propose to develop a digital atlas methodology that will be used to segment the cranial nerves from patient image data. The atlas will be created from high-resolution MRI data based on a discrete deformable contour model called 1-Simplex mesh. Each of the cranial nerves will be modeled using its centerline and radius information where the centerline is estimated in a semi-automatic approach by finding a shortest path between two user-defined end points. The cranial nerve atlas is then made more robust by integrating a Statistical Shape Model so that the atlas can identify and segment nerves from images characterized by artifacts or low resolution. To the best of our knowledge, no such digital atlas methodology exists for segmenting nerves cranial nerves from MRI data. Therefore, our proposed system has important benefits to the neurosurgical community

A Jones matrix formalism for simulating three-dimensional polarized light imaging of brain tissue

The neuroimaging technique three-dimensional polarized light imaging (3D-PLI) provides a high-resolution reconstruction of nerve fibres in human post-mortem brains. The orientations of the fibres are derived from birefringence measurements of histological brain sections assuming that the nerve fibres - consisting of an axon and a surrounding myelin sheath - are uniaxial birefringent and that the measured optic axis is oriented in direction of the nerve fibres (macroscopic model). Although experimental studies support this assumption, the molecular structure of the myelin sheath suggests that the birefringence of a nerve fibre can be described more precisely by multiple optic axes oriented radially around the fibre axis (microscopic model). In this paper, we compare the use of the macroscopic and the microscopic model for simulating 3D-PLI by means of the Jones matrix formalism. The simulations show that the macroscopic model ensures a reliable estimation of the fibre orientations as long as the polarimeter does not resolve structures smaller than the diameter of single fibres. In the case of fibre bundles, polarimeters with even higher resolutions can be used without losing reliability. When taking the myelin density into account, the derived fibre orientations are considerably improved.Comment: 20 pages, 8 figure

On Nature of the Gradient Echo MR Signal and Its Application to Monitoring Multiple Sclerosis

Multiple Sclerosis is a common disease, affecting 2.5 million people world-wide. The clinical course is heterogeneous, ranging from benign disease in which patients live an almost normal life to severe and devastating disease that may shorten life. Despite much research, a fully effective treatment for MS is still unavailable and diagnostic techniques for monitoring MS disease evolution are much needed. As a non-invasive tool, Magnetic resonance imaging: MRI) plays a key role in MS diagnosis. Numerous MRI techniques have been proposed over the years. Among most widely used are conventional T1-weighted: T1W), T2-weighted: T2W) and FLuid Attenuated Inversion Recovery: FLAIR) imaging techniques. However their results do not correlate well with neurological findings. Several advanced MRI techniques are also used as research tools to study MS. Among them are magnetization transfer contrast imaging: MT), MR spectroscopy: MRS), and Diffusion Tensor Imaging: DTI) but they have not penetrated to clinical arena yet. Gradient Echo Plural Contrast Imaging: GEPCI) developed in our laboratory is a post processing technique based on multi-echo gradient echo sequence. It offers basic contrasts such as T1W images and T2* maps obtained from magnitude of GEPCI signal, and frequency maps obtained from GEPCI signal phase. Phase information of Gradient Echo MR signal has recently attracted much attention of the MR community since it manifests superior gray matter/ white matter contrast and sub-cortical contrast, especially at high field: 7 T) MRI. However the nature of this contrast is under intense debates. Our group proposed a theoretical framework - Generalized Lorentzian Approach - which emphasizes that, contrary to a common-sense intuition, phase contrast in brain tissue is not directly proportional to the tissue bulk magnetic susceptibility but is rather determined by the geometrical arrangement of brain tissue components: lipids, proteins, iron, etc.) at the cellular and sub-cellular levels - brain tissue magnetic architecture . In this thesis we have provide first direct prove of this hypothesis by measurement of phase contrast in isolated optic nerve. We have also provided first quantitative measurements of the contribution to phase contrast from the water-macromolecule exchange effect. Based on our measurement in protein solutions, we demonstrated that the magnitude of exchange effect is 1/2 of susceptibility effect and to the opposite sign. GEPCI technique also offers a scoring method for monitoring Multiple Sclerosis based on the quantitative T2* maps generated from magnitude information of gradient echo signal. Herein we demonstrated a strong agreement between GEPCI quantitative scores and traditional lesion load assessment. We also established a correlation between GEPCI scores and clinical tests for MS patients. We showed that this correlation is stronger than that found between traditional lesion load and clinical tests. Such studies will be carried out for longer period and on MS subjects with broader range of disease severity in the future. We have also demonstrated that the magnitude and phase information available from GEPCI experiment can be combined in multiple ways to generate novel contrasts that can help with visualization of neurological brain abnormalities beyond Multiple Sclerosis. In summary, in this study, we 1) propose novel contrasts for GEPCI from its basic images; 2) investigate the biophysical mechanisms behind phase contrast; 3) evaluate the benefits of quantitative T2* map offered by GEPCI in monitoring disease of Multiple Sclerosis by comparing GEPCI results to clinical standard techniques; 4) apply our theoretical framework - Generalized Lorentzian Approach - to better understand phase contrast in MS lesions

Aberrant visual pathway development in albinism: from retina to cortex

Albinism refers to a group of genetic abnormalities in melanogenesis that are associated neuronal misrouting through the optic chiasm. Previous imaging studies have shown structural alterations at different points along the visual pathway of people with albinism (PWA) including foveal hypoplasia, optic nerve and chiasm size alterations and visual cortex reorganisation, but fail to provide a holistic in-vivo characterisation of the visual neurodevelopmental alterations from retina to visual cortex. We perform quantitative assessment of visual pathway structure and function in 23 PWA and 20 matched controls using optical coherence tomography (OCT), volumetric magnetic resonance imaging (MRI), diffusion tensor imaging and visual evoked potentials (VEP). PWA had a higher streamline decussation index (percentage of total tractography streamlines decussating at the chiasm) compared to controls (Z=-2.24, p=0.025), and streamline decussation index correlated weakly significantly with inter-hemispheric asymmetry measured using VEP (r=0.484, p=0.042). For PWA, a significant correlation was found between foveal development index and total number of streamlines (r=0.662, p less than 0.001). Optic nerve (p=0.001) and tract (p=0.010) width, and chiasm width (P less than 0.001), area (p=0.006) and volume (p=0.005), were significantly smaller in PWA compared to controls. Significant positive correlations were found between peri-papillary retinal nerve fibre layer thickness and optic nerve (r=0.642, p less than 0.001) and tract (r=0.663, p less than 0.001) width. Occipital pole cortical thickness was 6.88% higher (Z=-4.10, p less than 0.001) in PWA and was related to anterior visual pathway structures including foveal retinal pigment epithelium complex thickness (r=-0.579, p=0.005), optic disc (r=0.478, p=0.021) and rim areas (r=0.597, p=0.003). We were unable to demonstrate a significant relationship between OCT-derived foveal or optic nerve measures and MRI-derived chiasm size or streamline decussation index. Non-invasive imaging techniques demonstrate aberrant development throughout the visual pathways of PWA compared to controls. Our novel tractographic demonstration of altered chiasmatic decussation in PWA corresponds to VEP measured cortical asymmetry and is consistent with chiasmatic misrouting in albinism. We also demonstrate a significant relationship between retinal pigment epithelium and visual cortex thickness indicating that retinal pigmentation defects in albinism lead to downstream structural reorganisation of the visual cortex

Fusion based analysis of ophthalmologic image data

summary:The paper presents an overview of image analysis activities of the Brno DAR group in the medical application area of retinal imaging. Particularly, illumination correction and SNR enhancement by registered averaging as preprocessing steps are briefly described; further mono- and multimodal registration methods developed for specific types of ophthalmological images, and methods for segmentation of optical disc, retinal vessel tree and autofluorescence areas are presented. Finally, the designed methods for neural fibre layer detection and evaluation on retinal images, utilising different combined texture analysis approaches and several types of classifiers, are shown. The results in all the areas are shortly commented on at the respective sections. In order to emphasise methodological aspects, the methods and results are ordered according to consequential phases of processing rather then divided according to individual medical applications

Mri Methods For Imaging The Feto-Placental Vasculature And Blood

Fetal magnetic resonance imaging (MRI) in recent times has become a well-established adjunct to ultrasound (US) in routine clinical prenatal care and diagnostics. The majority of fetal MRI is restricted to T2-weighted scans, where the diagnosis is based on the appearance of normal and abnormal tissue. Although there have been many advancements in MRI and a plethora of sequences, that probe different anatomical and different physiological process, the adaptation of these in fetal imaging has been rather slow. Many of these can extract quantitative parameters that can throw light on the underlying tissue’s normal/patho-physiology. But the use of such quantitative MRI methods has been extremely limited in fetal imaging due to its unique and dynamic physiological milieu that pose several technical challenges including low signal to noise and/or resolution, artifacts associated with abdominal imaging and most importantly fetal motion. These limitations are expected to be overcome by (a) optimizing and (b) developing novel MR imaging sequences, both of which constitute the primary aim of my work. This work develops a framework that allows for vascular imaging in the fetus and placenta. This includes both qualitative vascular imaging and blood flow quantification. Towards this, three broad directions were explored (a) Moving to higher field imaging, while optimizing parameters for low energy deposition and (b) application of non-gated phase contrast MRI and (c) optimization of conventional time-of-flight angiography for fetal applications

Local volume fraction distributions of axons, astrocytes, and myelin in deep subcortical white matter

This study aims to statistically describe histologically stained white matter brain sections to subsequently inform and validate diffusion MRI techniques. For the first time, we characterise volume fraction distributions of three of the main structures in deep subcortical white matter (axons, astrocytes, and myelinated axons) in a representative cohort of an ageing population for which well-characterized neuropathology data is available. We analysed a set of samples from 90 subjects of the Cognitive Function and Ageing Study (CFAS), stratified into three groups of 30 subjects each, in relation to the presence of age-associated deep subcortical lesions. This provides volume fraction distributions in different scenarios relevant to brain diffusion MRI in dementia. We also assess statistically significant differences found between these groups. In agreement with previous literature, our results indicate that white matter lesions are related with a decrease in the myelinated axons fraction and an increase in astrocytic fraction, while no statistically significant changes occur in axonal mean fraction. In addition, we introduced a framework to quantify volume fraction distributions from 2D immunohistochemistry images, which is validated against in silico simulations. Since a trade-off between precision and resolution emerged, we also performed an assessment of the optimal scale for computing such distributions