23,643 research outputs found
Automatic Analysis of Brain Tissue and Structural Connectivity in MRI
Studies of the brain using magnetic resonance imaging (MRI) can provide
insights in physiology and pathology that can eventually aid clinical
diagnosis and therapy monitoring. MRI data acquired in these studies can
be difficult, as well as laborious, to interpret and analyze by human
observers. Moreover, analysis by human observers can hamper the
reproducibility by both inter- and intra-observer variability. These
studies do, therefore, require accurate and reproducible quantitative
image analysis techniques to optimally benefit from the valuable
information contained in the MRI data. In this thesis, we focus on the
development and evaluation of quantitative analysis techniques for brain
MRI data.
In the first part of this thesis, we focus on automatic brain tissue and
white matter lesion (WML) segmentation. We propose an automatic WML
segmentation method based on fluid-attenuated inversion recovery (FLAIR)
scans that can be added as an extension to brain tissue segmentation
methods. We optimize and evaluate a previously proposed automatic brain
tissue segmentation method in combination with the WML segmentation
extension. We compare the accuracy and reproducibility of this newly
developed segmentation framework to several other methods, some of which
are publicly available. Additionally, we compare two brain tissue
segmentation methods on the segmentation of longitudinal brain MRI data.
The second part of this thesis is about structural brain connectivity
based on diffusion MRI data. We propose a framework for analysis of
structural connectivity in large groups of subjects. Structural
connectivity is established using minimum cost paths based on the
diffusion weighted images and is summarized in brain networks. Using
statistical methods, we demonstrate that the obtained networks contain
information regarding subject age, white matter lesion load and white
matter atrophy. Finally, we evaluate the reproducibility of the proposed
brain connectivity framework
Adversarial training and dilated convolutions for brain MRI segmentation
Convolutional neural networks (CNNs) have been applied to various automatic
image segmentation tasks in medical image analysis, including brain MRI
segmentation. Generative adversarial networks have recently gained popularity
because of their power in generating images that are difficult to distinguish
from real images.
In this study we use an adversarial training approach to improve CNN-based
brain MRI segmentation. To this end, we include an additional loss function
that motivates the network to generate segmentations that are difficult to
distinguish from manual segmentations. During training, this loss function is
optimised together with the conventional average per-voxel cross entropy loss.
The results show improved segmentation performance using this adversarial
training procedure for segmentation of two different sets of images and using
two different network architectures, both visually and in terms of Dice
coefficients.Comment: MICCAI 2017 Workshop on Deep Learning in Medical Image Analysi
Scalable multimodal convolutional networks for brain tumour segmentation
Brain tumour segmentation plays a key role in computer-assisted surgery. Deep
neural networks have increased the accuracy of automatic segmentation
significantly, however these models tend to generalise poorly to different
imaging modalities than those for which they have been designed, thereby
limiting their applications. For example, a network architecture initially
designed for brain parcellation of monomodal T1 MRI can not be easily
translated into an efficient tumour segmentation network that jointly utilises
T1, T1c, Flair and T2 MRI. To tackle this, we propose a novel scalable
multimodal deep learning architecture using new nested structures that
explicitly leverage deep features within or across modalities. This aims at
making the early layers of the architecture structured and sparse so that the
final architecture becomes scalable to the number of modalities. We evaluate
the scalable architecture for brain tumour segmentation and give evidence of
its regularisation effect compared to the conventional concatenation approach.Comment: Paper accepted at MICCAI 201
Dilatation of Lateral Ventricles with Brain Volumes in Infants with 3D Transfontanelle US
Ultrasound (US) can be used to assess brain development in newborns, as MRI
is challenging due to immobilization issues, and may require sedation.
Dilatation of the lateral ventricles in the brain is a risk factor for poorer
neurodevelopment outcomes in infants. Hence, 3D US has the ability to assess
the volume of the lateral ventricles similar to clinically standard MRI, but
manual segmentation is time consuming. The objective of this study is to
develop an approach quantifying the ratio of lateral ventricular dilatation
with respect to total brain volume using 3D US, which can assess the severity
of macrocephaly. Automatic segmentation of the lateral ventricles is achieved
with a multi-atlas deformable registration approach using locally linear
correlation metrics for US-MRI fusion, followed by a refinement step using
deformable mesh models. Total brain volume is estimated using a 3D ellipsoid
modeling approach. Validation was performed on a cohort of 12 infants, ranging
from 2 to 8.5 months old, where 3D US and MRI were used to compare brain
volumes and segmented lateral ventricles. Automatically extracted volumes from
3D US show a high correlation and no statistically significant difference when
compared to ground truth measurements. Differences in volume ratios was 6.0 +/-
4.8% compared to MRI, while lateral ventricular segmentation yielded a mean
Dice coefficient of 70.8 +/- 3.6% and a mean absolute distance (MAD) of 0.88
+/- 0.2mm, demonstrating the clinical benefit of this tool in paediatric
ultrasound
Automatic MRI 2D Brain Segmentation using Graph SearchingTechnique
Accurate and efficient segmentation of the whole brain in magnetic resonance (MR) images is a key task in many neuroscience and medical studies either because the whole brain is the final anatomical structure of interest or because the automatic extraction facilitates further analysis. The problem of segmenting brain MRI images has been extensively addressed by many researchers. Despite the relevant achievements obtained, automated segmentation of brain MRI imagery is still a challenging problem whose solution has to cope with critical aspects such as anatomical variability and pathological deformation. In the present paper, we describe and experimentally evaluate a method for segmenting brain from MRI images basing on two-dimensional graph searching principles for border detection. The segmentation of the whole brain over the entire volume is accomplished slice by slice, automatically detecting frames including eyes. The method is fully automatic and easily reproducible by computing the internal main parameters directly from the image data. The segmentation procedure is conceived as a tool of general applicability, although design requirements are especially commensurate with the accuracy required in clinical tasks such as surgical planning and post-surgical assessment. Several experiments were performed to assess the performance of the algorithm on a varied set of MRI images obtaining good results in terms of accuracy and stabilit
Fully Automatic MRI Brain Tumor Segmentation
Today in the area of medical research, the care of brain tumor patient attracts a lot of attention. Brain tumor segmentation consists of separating the different brain tumor tissues from normal tissues. In the past, many researchers in the field of medical imaging and soft computing have made significant survey in the field of brain tumor segmentation. Both semiautomatic and fully automatic methods have been proposed. Clinical acceptance of segmentation techniques has depended on the simplicity of the segmentation and the degree of user supervision. Additionally, with the development of particular software tools for automatic segmentation and brain tumor detection, which reduce the doctors’ time spent on manual segmentation, more effective and efficient results are provided. In this paper BraTumIA software tool has been used for automated segmentation on MRI brain tumor images in order to perform fully segmentation by separating different brain tumor tissues from the normal ones
- …