2,528 research outputs found
Unsupervised Multi Class Segmentation of 3D Images with Intensity Inhomogeneities
Intensity inhomogeneities in images constitute a considerable challenge in
image segmentation. In this paper we propose a novel biconvex variational model
to tackle this task. We combine a total variation approach for multi class
segmentation with a multiplicative model to handle the inhomogeneities. Our
method assumes that the image intensity is the product of a smoothly varying
part and a component which resembles important image structures such as edges.
Therefore, we penalize in addition to the total variation of the label
assignment matrix a quadratic difference term to cope with the smoothly varying
factor. A critical point of our biconvex functional is computed by a modified
proximal alternating linearized minimization method (PALM). We show that the
assumptions for the convergence of the algorithm are fulfilled by our model.
Various numerical examples demonstrate the very good performance of our method.
Particular attention is paid to the segmentation of 3D FIB tomographical images
which was indeed the motivation of our work
Serial Correlations in Single-Subject fMRI with Sub-Second TR
When performing statistical analysis of single-subject fMRI data, serial
correlations need to be taken into account to allow for valid inference.
Otherwise, the variability in the parameter estimates might be under-estimated
resulting in increased false-positive rates. Serial correlations in fMRI data
are commonly characterized in terms of a first-order autoregressive (AR)
process and then removed via pre-whitening. The required noise model for the
pre-whitening depends on a number of parameters, particularly the repetition
time (TR). Here we investigate how the sub-second temporal resolution provided
by simultaneous multislice (SMS) imaging changes the noise structure in fMRI
time series. We fit a higher-order AR model and then estimate the optimal AR
model order for a sequence with a TR of less than 600 ms providing whole brain
coverage. We show that physiological noise modelling successfully reduces the
required AR model order, but remaining serial correlations necessitate an
advanced noise model. We conclude that commonly used noise models, such as the
AR(1) model, are inadequate for modelling serial correlations in fMRI using
sub-second TRs. Rather, physiological noise modelling in combination with
advanced pre-whitening schemes enable valid inference in single-subject
analysis using fast fMRI sequences
Stabilised bias field: segmentation with intensity inhomogeneity
Automatic segmentation in the variational framework is a challenging task within the field of imaging sciences. Achieving robustness is a major problem, particularly for images with high levels of intensity inhomogeneity. The two-phase piecewise-constant case of the Mumford-Shah formulation is most suitable for images with simple and homogeneous features where the intensity variation is limited. However, it has been applied to many different types of synthetic and real images after some adjustments to the formulation. Recent work has incorporated bias field estimation to allow for intensity inhomogeneity, with great success in terms of segmentation quality. However, the framework and assumptions involved lead to inconsistencies in the method that can adversely affect results. In this paper we address the task of generalising the piecewise-constant formulation, to approximate minimisers of the original Mumford-Shah formulation. We first review existing methods for treating inhomogeneity, and demonstrate the inconsistencies with the bias field estimation framework. We propose a modified variational model to account for these problems by introducing an additional constraint, and detail how the exact minimiser can be approximated in the context of this new formulation. We extend this concept to selective segmentation with the introduction of a distance selection term. These models are minimised with convex relaxation methods, where the global minimiser can be found for a fixed fitting term. Finally, we present numerical results that demonstrate an improvement to existing methods in terms of reliability and parameter dependence, and results for selective segmentation in the case of intensity inhomogeneity. </jats:p
A Geometric Flow Approach for Segmentation of Images with Inhomongeneous Intensity and Missing Boundaries
Image segmentation is a complex mathematical problem, especially for images
that contain intensity inhomogeneity and tightly packed objects with missing
boundaries in between. For instance, Magnetic Resonance (MR) muscle images
often contain both of these issues, making muscle segmentation especially
difficult. In this paper we propose a novel intensity correction and a
semi-automatic active contour based segmentation approach. The approach uses a
geometric flow that incorporates a reproducing kernel Hilbert space (RKHS) edge
detector and a geodesic distance penalty term from a set of markers and
anti-markers. We test the proposed scheme on MR muscle segmentation and compare
with some state of the art methods. To help deal with the intensity
inhomogeneity in this particular kind of image, a new approach to estimate the
bias field using a fat fraction image, called Prior Bias-Corrected Fuzzy
C-means (PBCFCM), is introduced. Numerical experiments show that the proposed
scheme leads to significantly better results than compared ones. The average
dice values of the proposed method are 92.5%, 85.3%, 85.3% for quadriceps,
hamstrings and other muscle groups while other approaches are at least 10%
worse.Comment: Presented at CVIT 2023 Conference. Accepted to Journal of Image and
Graphic
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
Level set segmentation using non-negative matrix factorization with application to brain MRI
We address the problem of image segmentation using a new deformable model based on the level set method (LSM) and non-negative matrix factorization (NMF). We describe the use of NMF to reduce the dimension of large images from thousands of pixels to a handful of metapixels or regions. In addition, the exact number of regions is discovered using the nuclear norm of the NMF factors. The proposed NMF-LSM characterizes the histogram of the image, calculated over the image blocks, as nonnegative combinations of basic histograms computed using NMF (V ~ W H). The matrix W represents the histograms of the image regions, whereas the matrix H provides the spatial clustering of the regions. NMF-LSM takes into account the bias field present particularly in medical images. We define two local clustering criteria in terms of the NMF factors. The first criterion defines a local intensity clustering property based on the matrix W by computing the average intensity and standard deviation of every region. The second criterion defines a local spatial clustering using the matrix H. The local clustering is then summed over all regions to give a global criterion of image segmentation. In LSM, these criteria define an energy minimized w.r.t. LSFs and the bias field to achieve the segmentation. The proposed method is validated on synthetic binary and gray-scale images, and then applied to real brain MRI images. NMF-LSM provides a general approach for robust region discovery and segmentation in heterogeneous images
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