2,796 research outputs found
PSACNN: Pulse Sequence Adaptive Fast Whole Brain Segmentation
With the advent of convolutional neural networks~(CNN), supervised learning
methods are increasingly being used for whole brain segmentation. However, a
large, manually annotated training dataset of labeled brain images required to
train such supervised methods is frequently difficult to obtain or create. In
addition, existing training datasets are generally acquired with a homogeneous
magnetic resonance imaging~(MRI) acquisition protocol. CNNs trained on such
datasets are unable to generalize on test data with different acquisition
protocols. Modern neuroimaging studies and clinical trials are necessarily
multi-center initiatives with a wide variety of acquisition protocols. Despite
stringent protocol harmonization practices, it is very difficult to standardize
the gamut of MRI imaging parameters across scanners, field strengths, receive
coils etc., that affect image contrast. In this paper we propose a CNN-based
segmentation algorithm that, in addition to being highly accurate and fast, is
also resilient to variation in the input acquisition. Our approach relies on
building approximate forward models of pulse sequences that produce a typical
test image. For a given pulse sequence, we use its forward model to generate
plausible, synthetic training examples that appear as if they were acquired in
a scanner with that pulse sequence. Sampling over a wide variety of pulse
sequences results in a wide variety of augmented training examples that help
build an image contrast invariant model. Our method trains a single CNN that
can segment input MRI images with acquisition parameters as disparate as
-weighted and -weighted contrasts with only -weighted training
data. The segmentations generated are highly accurate with state-of-the-art
results~(overall Dice overlap), with a fast run time~( 45
seconds), and consistent across a wide range of acquisition protocols.Comment: Typo in author name corrected. Greves -> Grev
Fiber Orientation Estimation Guided by a Deep Network
Diffusion magnetic resonance imaging (dMRI) is currently the only tool for
noninvasively imaging the brain's white matter tracts. The fiber orientation
(FO) is a key feature computed from dMRI for fiber tract reconstruction.
Because the number of FOs in a voxel is usually small, dictionary-based sparse
reconstruction has been used to estimate FOs with a relatively small number of
diffusion gradients. However, accurate FO estimation in regions with complex FO
configurations in the presence of noise can still be challenging. In this work
we explore the use of a deep network for FO estimation in a dictionary-based
framework and propose an algorithm named Fiber Orientation Reconstruction
guided by a Deep Network (FORDN). FORDN consists of two steps. First, we use a
smaller dictionary encoding coarse basis FOs to represent the diffusion
signals. To estimate the mixture fractions of the dictionary atoms (and thus
coarse FOs), a deep network is designed specifically for solving the sparse
reconstruction problem. Here, the smaller dictionary is used to reduce the
computational cost of training. Second, the coarse FOs inform the final FO
estimation, where a larger dictionary encoding dense basis FOs is used and a
weighted l1-norm regularized least squares problem is solved to encourage FOs
that are consistent with the network output. FORDN was evaluated and compared
with state-of-the-art algorithms that estimate FOs using sparse reconstruction
on simulated and real dMRI data, and the results demonstrate the benefit of
using a deep network for FO estimation.Comment: A shorter version is accepted by MICCAI 201
Persistent Homology in Sparse Regression and its Application to Brain Morphometry
Sparse systems are usually parameterized by a tuning parameter that
determines the sparsity of the system. How to choose the right tuning parameter
is a fundamental and difficult problem in learning the sparse system. In this
paper, by treating the the tuning parameter as an additional dimension,
persistent homological structures over the parameter space is introduced and
explored. The structures are then further exploited in speeding up the
computation using the proposed soft-thresholding technique. The topological
structures are further used as multivariate features in the tensor-based
morphometry (TBM) in characterizing white matter alterations in children who
have experienced severe early life stress and maltreatment. These analyses
reveal that stress-exposed children exhibit more diffuse anatomical
organization across the whole white matter region.Comment: submitted to IEEE Transactions on Medical Imagin
A Survey on Deep Learning in Medical Image Analysis
Deep learning algorithms, in particular convolutional networks, have rapidly
become a methodology of choice for analyzing medical images. This paper reviews
the major deep learning concepts pertinent to medical image analysis and
summarizes over 300 contributions to the field, most of which appeared in the
last year. We survey the use of deep learning for image classification, object
detection, segmentation, registration, and other tasks and provide concise
overviews of studies per application area. Open challenges and directions for
future research are discussed.Comment: Revised survey includes expanded discussion section and reworked
introductory section on common deep architectures. Added missed papers from
before Feb 1st 201
Automated Gene Classification using Nonnegative Matrix Factorization on Biomedical Literature
Understanding functional gene relationships is a challenging problem for biological applications. High-throughput technologies such as DNA microarrays have inundated biologists with a wealth of information, however, processing that information remains problematic. To help with this problem, researchers have begun applying text mining techniques to the biological literature. This work extends previous work based on Latent Semantic Indexing (LSI) by examining Nonnegative Matrix Factorization (NMF). Whereas LSI incorporates the singular value decomposition (SVD) to approximate data in a dense, mixed-sign space, NMF produces a parts-based factorization that is directly interpretable. This space can, in theory, be used to augment existing ontologies and annotations by identifying themes within the literature. Of course, performing NMF does not come without a price—namely, the large number of parameters. This work attempts to analyze the effects of some of the NMF parameters on both convergence and labeling accuracy. Since there is a dearth of automated label evaluation techniques as well as “gold standard” hierarchies, a method to produce “correct” trees is proposed as well as a technique to label trees and to evaluate those labels
Development of Advanced, Clinically Feasible Neuroimaging Methodology with Diffusional Kurtosis Imaging
Diffusion MRI (dMRI) is a powerful, non-invasive tool for probing the structural organization of the human brain. Quantitative dMRI analyses provide unique capabilities for the characterization of tissue microstructure as well as imaging contrast that is not available to other modalities. White matter tractography relies on dMRI and is currently the only non-invasive technique for mapping structural connections in the human brain. In this chapter, we will describe diffusional kurtosis imaging, an effective and versatile dMRI technique, and discuss a clinical problem in temporal lobe epilepsy (TLE) which is insurmountable with current diagnostic approaches. Subsequent chapters will further develop the capabilities of DKI and demonstrate how it may be particularly well suited to overcome current barriers to care in the clinical management of TLE
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