4,438 research outputs found
Sub-cortical brain structure segmentation using F-CNN's
In this paper we propose a deep learning approach for segmenting sub-cortical
structures of the human brain in Magnetic Resonance (MR) image data. We draw
inspiration from a state-of-the-art Fully-Convolutional Neural Network (F-CNN)
architecture for semantic segmentation of objects in natural images, and adapt
it to our task. Unlike previous CNN-based methods that operate on image
patches, our model is applied on a full blown 2D image, without any alignment
or registration steps at testing time. We further improve segmentation results
by interpreting the CNN output as potentials of a Markov Random Field (MRF),
whose topology corresponds to a volumetric grid. Alpha-expansion is used to
perform approximate inference imposing spatial volumetric homogeneity to the
CNN priors. We compare the performance of the proposed pipeline with a similar
system using Random Forest-based priors, as well as state-of-art segmentation
algorithms, and show promising results on two different brain MRI datasets.Comment: ISBI 2016: International Symposium on Biomedical Imaging, Apr 2016,
Prague, Czech Republi
Bayesian Spatial Binary Regression for Label Fusion in Structural Neuroimaging
Many analyses of neuroimaging data involve studying one or more regions of
interest (ROIs) in a brain image. In order to do so, each ROI must first be
identified. Since every brain is unique, the location, size, and shape of each
ROI varies across subjects. Thus, each ROI in a brain image must either be
manually identified or (semi-) automatically delineated, a task referred to as
segmentation. Automatic segmentation often involves mapping a previously
manually segmented image to a new brain image and propagating the labels to
obtain an estimate of where each ROI is located in the new image. A more recent
approach to this problem is to propagate labels from multiple manually
segmented atlases and combine the results using a process known as label
fusion. To date, most label fusion algorithms either employ voting procedures
or impose prior structure and subsequently find the maximum a posteriori
estimator (i.e., the posterior mode) through optimization. We propose using a
fully Bayesian spatial regression model for label fusion that facilitates
direct incorporation of covariate information while making accessible the
entire posterior distribution. We discuss the implementation of our model via
Markov chain Monte Carlo and illustrate the procedure through both simulation
and application to segmentation of the hippocampus, an anatomical structure
known to be associated with Alzheimer's disease.Comment: 24 pages, 10 figure
Quantitative magnetic resonance image analysis via the EM algorithm with stochastic variation
Quantitative Magnetic Resonance Imaging (qMRI) provides researchers insight
into pathological and physiological alterations of living tissue, with the help
of which researchers hope to predict (local) therapeutic efficacy early and
determine optimal treatment schedule. However, the analysis of qMRI has been
limited to ad-hoc heuristic methods. Our research provides a powerful
statistical framework for image analysis and sheds light on future localized
adaptive treatment regimes tailored to the individual's response. We assume in
an imperfect world we only observe a blurred and noisy version of the
underlying pathological/physiological changes via qMRI, due to measurement
errors or unpredictable influences. We use a hidden Markov random field to
model the spatial dependence in the data and develop a maximum likelihood
approach via the Expectation--Maximization algorithm with stochastic variation.
An important improvement over previous work is the assessment of variability in
parameter estimation, which is the valid basis for statistical inference. More
importantly, we focus on the expected changes rather than image segmentation.
Our research has shown that the approach is powerful in both simulation studies
and on a real dataset, while quite robust in the presence of some model
assumption violations.Comment: Published in at http://dx.doi.org/10.1214/07-AOAS157 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
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