1,209 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
Deep learning-based parameter mapping for joint relaxation and diffusion tensor MR Fingerprinting
Magnetic Resonance Fingerprinting (MRF) enables the simultaneous
quantification of multiple properties of biological tissues. It relies on a
pseudo-random acquisition and the matching of acquired signal evolutions to a
precomputed dictionary. However, the dictionary is not scalable to
higher-parametric spaces, limiting MRF to the simultaneous mapping of only a
small number of parameters (proton density, T1 and T2 in general). Inspired by
diffusion-weighted SSFP imaging, we present a proof-of-concept of a novel MRF
sequence with embedded diffusion-encoding gradients along all three axes to
efficiently encode orientational diffusion and T1 and T2 relaxation. We take
advantage of a convolutional neural network (CNN) to reconstruct multiple
quantitative maps from this single, highly undersampled acquisition. We bypass
expensive dictionary matching by learning the implicit physical relationships
between the spatiotemporal MRF data and the T1, T2 and diffusion tensor
parameters. The predicted parameter maps and the derived scalar diffusion
metrics agree well with state-of-the-art reference protocols. Orientational
diffusion information is captured as seen from the estimated primary diffusion
directions. In addition to this, the joint acquisition and reconstruction
framework proves capable of preserving tissue abnormalities in multiple
sclerosis lesions
Informative sample generation using class aware generative adversarial networks for classification of chest Xrays
Training robust deep learning (DL) systems for disease detection from medical
images is challenging due to limited images covering different disease types
and severity. The problem is especially acute, where there is a severe class
imbalance. We propose an active learning (AL) framework to select most
informative samples for training our model using a Bayesian neural network.
Informative samples are then used within a novel class aware generative
adversarial network (CAGAN) to generate realistic chest xray images for data
augmentation by transferring characteristics from one class label to another.
Experiments show our proposed AL framework is able to achieve state-of-the-art
performance by using about of the full dataset, thus saving significant
time and effort over conventional methods
Prior-based Coregistration and Cosegmentation
We propose a modular and scalable framework for dense coregistration and
cosegmentation with two key characteristics: first, we substitute ground truth
data with the semantic map output of a classifier; second, we combine this
output with population deformable registration to improve both alignment and
segmentation. Our approach deforms all volumes towards consensus, taking into
account image similarities and label consistency. Our pipeline can incorporate
any classifier and similarity metric. Results on two datasets, containing
annotations of challenging brain structures, demonstrate the potential of our
method.Comment: The first two authors contributed equall
Multi-Atlas Segmentation using Partially Annotated Data: Methods and Annotation Strategies
Multi-atlas segmentation is a widely used tool in medical image analysis,
providing robust and accurate results by learning from annotated atlas
datasets. However, the availability of fully annotated atlas images for
training is limited due to the time required for the labelling task.
Segmentation methods requiring only a proportion of each atlas image to be
labelled could therefore reduce the workload on expert raters tasked with
annotating atlas images. To address this issue, we first re-examine the
labelling problem common in many existing approaches and formulate its solution
in terms of a Markov Random Field energy minimisation problem on a graph
connecting atlases and the target image. This provides a unifying framework for
multi-atlas segmentation. We then show how modifications in the graph
configuration of the proposed framework enable the use of partially annotated
atlas images and investigate different partial annotation strategies. The
proposed method was evaluated on two Magnetic Resonance Imaging (MRI) datasets
for hippocampal and cardiac segmentation. Experiments were performed aimed at
(1) recreating existing segmentation techniques with the proposed framework and
(2) demonstrating the potential of employing sparsely annotated atlas data for
multi-atlas segmentation
Automated Segmentation of the Pericardium Using a Feature Based Multi-atlas Approach
Multi-atlas segmentation is a widely used method that has proved to work well for the problem of segmenting organs in medical images. But standard methods are time consuming and the amount of data quickly grows to a point making use of these methods intractable. In this work we present a fully automatic method for segmentation of the pericardium in 3D CTA-images. We use a multi-atlas approach based on feature based registration (SURF) and use RANSAC to handle the large amount of outliers. The multi-atlas votes are fused by incorporating them into an MRF together with the intensity information of the target image and the optimal segmentation is found efficiently using graph cuts. We evaluate our method on a set of 10 CTA-volumes with manual expert delineation of the pericardium and we show that our method provides comparable results to a standard multi-atlas algorithm but at a large gain in computational efficiency
Generative Models for Preprocessing of Hospital Brain Scans
I will in this thesis present novel computational methods for processing routine clinical brain scans. Such scans were originally acquired for qualitative assessment by trained radiologists, and present a number of difficulties for computational models, such as those within common neuroimaging analysis software. The overarching objective of this work is to enable efficient and fully automated analysis of large neuroimaging datasets, of the type currently present in many hospitals worldwide. The methods presented are based on probabilistic, generative models of the observed imaging data, and therefore rely on informative priors and realistic forward models. The first part of the thesis will present a model for image quality improvement, whose key component is a novel prior for multimodal datasets. I will demonstrate its effectiveness for super-resolving thick-sliced clinical MR scans and for denoising CT images and MR-based, multi-parametric mapping acquisitions. I will then show how the same prior can be used for within-subject, intermodal image registration, for more robustly registering large numbers of clinical scans. The second part of the thesis focusses on improved, automatic segmentation and spatial normalisation of routine clinical brain scans. I propose two extensions to a widely used segmentation technique. First, a method for this model to handle missing data, which allows me to predict entirely missing modalities from one, or a few, MR contrasts. Second, a principled way of combining the strengths of probabilistic, generative models with the unprecedented discriminative capability of deep learning. By introducing a convolutional neural network as a Markov random field prior, I can model nonlinear class interactions and learn these using backpropagation. I show that this model is robust to sequence and scanner variability. Finally, I show examples of fitting a population-level, generative model to various neuroimaging data, which can model, e.g., CT scans with haemorrhagic lesions
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