102 research outputs found
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
Automated Morphometric Characterization of the Cerebral Cortex for the Developing and Ageing Brain
Morphometric characterisation of the cerebral cortex can provide information about patterns of brain development and ageing and may be relevant for diagnosis and estimation of the progression of diseases such as Alzheimer's, Huntington's, and schizophrenia. Therefore, understanding and describing the differences between populations in terms of structural volume, shape and thickness is of critical importance. Methodologically, due to data quality, presence of noise, PV effects, limited resolution and pathological variability, the automated, robust and time-consistent estimation of morphometric features is still an unsolved problem. This thesis focuses on the development of tools for robust cross-sectional and longitudinal morphometric characterisation of the human cerebral cortex. It describes techniques for tissue segmentation, structural and morphometric characterisation, cross-sectional and longitudinally cortical thickness estimation from serial MRI images in both adults and neonates. Two new probabilistic brain tissue segmentation techniques are introduced in order to accurately and robustly segment the brain of elderly and neonatal subjects, even in the presence of marked pathology. Two other algorithms based on the concept of multi-atlas segmentation propagation and fusion are also introduced in order to parcelate the brain into its multiple composing structures with the highest possible segmentation accuracy. Finally, we explore the use of the Khalimsky cubic complex framework for the extraction of topologically correct thickness measurements from probabilistic segmentations without explicit parametrisation of the edge. A longitudinal extension of this method is also proposed. The work presented in this thesis has been extensively validated on elderly and neonatal data from several scanners, sequences and protocols. The proposed algorithms have also been successfully applied to breast and heart MRI, neck and colon CT and also to small animal imaging. All the algorithms presented in this thesis are available as part of the open-source package NiftySeg
Recommended from our members
State of the Art of Level Set Methods in Segmentation and Registration of Medical Imaging Modalities
Segmentation of medical images is an important step in various applications such as visualization, quantitative analysis and image-guided surgery. Numerous segmentation methods have been developed in the past two decades for extraction of organ contours on medical images. Low-level segmentation methods, such as pixel-based clustering, region growing, and filter-based edge detection, require additional pre-processing and post-processing as well as considerable amounts of expert intervention or information of the objects of interest. Furthermore the subsequent analysis of segmented objects is hampered by the primitive, pixel or voxel level representations from those region-based segmentation. Deformable models, on the other hand, provide an explicit representation of the boundary and the shape of the object. They combine several desirable features such as inherent connectivity and smoothness, which counteract noise and boundary irregularities, as well as the ability to incorporate knowledge about the object of interest. However, parametric deformable models have two main limitations. First, in situations where the initial model and desired object boundary differ greatly in size and shape, the model must be re-parameterized dynamically to faithfully recover the object boundary. The second limitation is that it has difficulty dealing with topological adaptation such as splitting or merging model parts, a useful property for recovering either multiple objects or objects with unknown topology. This difficulty is caused by the fact that a new parameterization must be constructed whenever topology change occurs, which requires sophisticated schemes. Level set deformable models, also referred to as geometric deformable models, provide an elegant solution to address the primary limitations of parametric deformable models. These methods have drawn a great deal of attention since their introduction in 1988. Advantages of the contour implicit formulation of the deformable model over parametric formulation include: (1) no parameterization of the contour, (2) topological flexibility, (3) good numerical stability, (4) straightforward extension of the 2D formulation to n-D. Recent reviews on the subject include papers from Suri. In this chapter we give a general overview of the level set segmentation methods with emphasize on new frameworks recently introduced in the context of medical imaging problems. We then introduce novel approaches that aim at combining segmentation and registration in a level set formulation. Finally we review a selective set of clinical works with detailed validation of the level set methods for several clinical applications
Do informal caregivers of people with dementia mirror the cognitive deficits of their demented patients?:A pilot study
Recent research suggests that informal caregivers of people with dementia (ICs) experience more cognitive deficits than noncaregivers. The reason for this is not yet clear. Objective: to test the hypothesis that ICs ‘mirror' the cognitive deficits of the demented people they care for. Participants and methods: 105 adult ICs were asked to complete three neuropsychological tests: letter fluency, category fluency, and the logical memory test from the WMS-III. The ICs were grouped according to the diagnosis of their demented patients. One-sample ttests were conducted to investigate if the standardized mean scores (t-scores) of the ICs were different from normative data. A Bonferroni correction was used to correct for multiple comparisons. Results: 82 ICs cared for people with Alzheimer's dementia and 23 ICs cared for people with vascular dementia. Mean letter fluency score of the ICs of people with Alzheimer's dementia was significantly lower than the normative mean letter fluency score, p = .002. The other tests yielded no significant results. Conclusion: our data shows that ICs of Alzheimer patients have cognitive deficits on the letter fluency test. This test primarily measures executive functioning and it has been found to be sensitive to mild cognitive impairment in recent research. Our data tentatively suggests that ICs who care for Alzheimer patients also show signs of cognitive impairment but that it is too early to tell if this is cause for concern or not
Doctor of Philosophy
dissertationMagnetic Resonance (MR) is a relatively risk-free and flexible imaging modality that is widely used for studying the brain. Biophysical and chemical properties of brain tissue are captured by intensity measurements in T1W (T1-Weighted) and T2W (T2-Weighted) MR scans. Rapid maturational processes taking place in the infant brain manifest as changes in co{\tiny }ntrast between white matter and gray matter tissue classes in these scans. However, studies based on MR image appearance face severe limitations due to the uncalibrated nature of MR intensity and its variability with respect to changing conditions of scan. In this work, we develop a method for studying the intensity variations between brain white matter and gray matter that are observed during infant brain development. This method is referred to by the acronym WIVID (White-gray Intensity Variation in Infant Development). WIVID is computed by measuring the Hellinger Distance of separation between intensity distributions of WM (White Matter) and GM (Gray Matter) tissue classes. The WIVID measure is shown to be relatively stable to interscan variations compared with raw signal intensity and does not require intensity normalization. In addition to quantification of tissue appearance changes using the WIVID measure, we test and implement a statistical framework for modeling temporal changes in this measure. WIVID contrast values are extracted from MR scans belonging to large-scale, longitudinal, infant brain imaging studies and modeled using the NLME (Nonlinear Mixed Effects) method. This framework generates a normative model of WIVID contrast changes with time, which captures brain appearance changes during neurodevelopment. Parameters from the estimated trajectories of WIVID contrast change are analyzed across brain lobes and image modalities. Parameters associated with the normative model of WIVID contrast change reflect established patterns of region-specific and modality-specific maturational sequences. We also detect differences in WIVID contrast change trajectories between distinct population groups. These groups are categorized based on sex and risk/diagnosis for ASD (Autism Spectrum Disorder). As a result of this work, the usage of the proposed WIVID contrast measure as a novel neuroimaging biomarker for characterizing tissue appearance is validated, and the clinical potential of the developed framework is demonstrated
Assessment and optimisation of MRI measures of atrophy as potential markers of disease progression in multiple sclerosis
There is a need for sensitive measures of disease progression in multiple sclerosis (MS) to
monitor treatment effects and understand disease evolution. MRI measures of brain
atrophy have been proposed for this purpose. This thesis investigates a number of
measurement techniques to assess their relative ability to monitor disease progression in
clinically isolated syndromes (CIS) and early relapsing remitting MS (RRMS).
Presented, is work demonstrating that measurement techniques and MR acquisitions can
be optimised to give small but significant improvements in measurement sensitivity and
precision, which provided greater statistical power. Direct comparison of numerous
techniques demonstrated significant differences between them. Atrophy measurements
from SIENA and the BBSI (registration-based techniques) were significantly more
precise than segmentation and subtraction of brain volumes, although larger percentage
losses were observed in grey matter fraction. Ventricular enlargement (VE) gave similar
statistical power and these techniques were robust and reliable; scan-rescan measurement
error was <0.01% of brain volume for BBSI and SIENA and <0.04ml for VE.
Annual atrophy rates (using SIENA) were -0.78% in RRMS and -0.52% in CIS patients
who progressed to MS, which were significantly greater than the rate observed in controls
(-0.07%). Sample size calculations for future trials of disease-modifying treatments in
RRMS, using brain atrophy as an outcome measure, are described. For SIENA, the BBSI
and VE respectively, an estimated 123, 157 and 140 patients per treatment arm
respectively would be required to show a 30% slowing of atrophy rate over two years. In
CIS subjects brain atrophy rate was a significant prognostic factor, independent of T2
MRI lesions at baseline, for development of MS by five year follow-up. It was also the
most significant MR predictor of disability in RRMS subjects. Cognitive assessment of
RRMS patients at five year follow-up is described, and brain atrophy rate was a
significant predictor of overall cognitive performance, and more specifically, of
performance in tests of memory.
The work in this thesis has identified methods for sensitively measuring progressive brain
atrophy in MS. It has shown that brain atrophy changes in early MS are related to early
clinical evolution, providing complementary information to clinical assessment that could
be utilised to monitor disease progression
Dimensionality reduction and unsupervised learning techniques applied to clinical psychiatric and neuroimaging phenotypes
Unsupervised learning and other multivariate analysis techniques are increasingly recognized in neuropsychiatric research. Here, finite mixture models and random forests were applied to clinical observations of patients with major depression to detect and validate treatment response subgroups. Further, independent component analysis and agglomerative hierarchical clustering were combined to build a brain parcellation solely on structural covariance information of magnetic resonance brain images. Übersetzte Kurzfassung: Unüberwachtes Lernen und andere multivariate Analyseverfahren werden zunehmend auf neuropsychiatrische Fragestellungen angewendet. Finite mixture Modelle wurden auf klinische Skalen von Patienten mit schwerer Depression appliziert, um Therapieantwortklassen zu bilden und mit Random Forests zu validieren. Unabhängigkeitsanalysen und agglomeratives hierarchisches Clustering wurden kombiniert, um die strukturelle Kovarianz von Magnetresonanztomographie-Bildern für eine Hirnparzellierung zu nutzen
- …