2,051 research outputs found
Multi-coil magnetic resonance imaging reconstruction with a Markov Random Field prior
Recent improvements in magnetic resonance image (MRI) reconstruction from partial data have been reported using spatial context modelling with Markov random field (MRF) priors. However, these algorithms have been developed only for magnitude images from single-coil measurements. In practice, most of the MRI images today are acquired using multi-coil data. In this paper, we extend our recent approach for MRI reconstruction with MRF priors to deal with multi-coil data i.e., to be applicable in parallel MRI (pMRI) settings. Instead of reconstructing images from different coils independently and subsequently combining them into the final image, we recover MRI image by processing jointly the undersampled measurements from all coils together with their estimated sensitivity maps. The proposed method incorporates a Bayesian formulation of the spatial context into the reconstruction problem. To solve the resulting problem, we derive an efficient algorithm based on the alternating direction method of multipliers (ADMM). Experimental results demonstrate the effectiveness of the proposed approach in comparison to some well-adopted methods for accelerated pMRI reconstruction from undersampled data
MRI reconstruction using Markov random field and total variation as composite prior
Reconstruction of magnetic resonance images (MRI) benefits from incorporating a priori knowledge about statistical dependencies among the representation coefficients. Recent results demonstrate that modeling intraband dependencies with Markov Random Field (MRF) models enable superior reconstructions compared to inter-scale models. In this paper, we develop a novel reconstruction method, which includes a composite prior based on an MRF model and Total Variation (TV). We use an anisotropic MRF model and propose an original data-driven method for the adaptive estimation of its parameters. From a Bayesian perspective, we define a new position-dependent type of regularization and derive a compact reconstruction algorithm with a novel soft-thresholding rule. Experimental results show the effectiveness of this method compared to the state of the art in the field
Monte Carlo-based Noise Compensation in Coil Intensity Corrected Endorectal MRI
Background: Prostate cancer is one of the most common forms of cancer found
in males making early diagnosis important. Magnetic resonance imaging (MRI) has
been useful in visualizing and localizing tumor candidates and with the use of
endorectal coils (ERC), the signal-to-noise ratio (SNR) can be improved. The
coils introduce intensity inhomogeneities and the surface coil intensity
correction built into MRI scanners is used to reduce these inhomogeneities.
However, the correction typically performed at the MRI scanner level leads to
noise amplification and noise level variations. Methods: In this study, we
introduce a new Monte Carlo-based noise compensation approach for coil
intensity corrected endorectal MRI which allows for effective noise
compensation and preservation of details within the prostate. The approach
accounts for the ERC SNR profile via a spatially-adaptive noise model for
correcting non-stationary noise variations. Such a method is useful
particularly for improving the image quality of coil intensity corrected
endorectal MRI data performed at the MRI scanner level and when the original
raw data is not available. Results: SNR and contrast-to-noise ratio (CNR)
analysis in patient experiments demonstrate an average improvement of 11.7 dB
and 11.2 dB respectively over uncorrected endorectal MRI, and provides strong
performance when compared to existing approaches. Conclusions: A new noise
compensation method was developed for the purpose of improving the quality of
coil intensity corrected endorectal MRI data performed at the MRI scanner
level. We illustrate that promising noise compensation performance can be
achieved for the proposed approach, which is particularly important for
processing coil intensity corrected endorectal MRI data performed at the MRI
scanner level and when the original raw data is not available.Comment: 23 page
A Bayesian approach for energy-based estimation of acoustic aberrations in high intensity focused ultrasound treatment
High intensity focused ultrasound is a non-invasive method for treatment of
diseased tissue that uses a beam of ultrasound to generate heat within a small
volume. A common challenge in application of this technique is that
heterogeneity of the biological medium can defocus the ultrasound beam. Here we
reduce the problem of refocusing the beam to the inverse problem of estimating
the acoustic aberration due to the biological tissue from acoustic radiative
force imaging data. We solve this inverse problem using a Bayesian framework
with a hierarchical prior and solve the inverse problem using a
Metropolis-within-Gibbs algorithm. The framework is tested using both synthetic
and experimental datasets. We demonstrate that our approach has the ability to
estimate the aberrations using small datasets, as little as 32 sonication
tests, which can lead to significant speedup in the treatment process.
Furthermore, our approach is compatible with a wide range of sonication tests
and can be applied to other energy-based measurement techniques
Joint Total Variation ESTATICS for Robust Multi-Parameter Mapping
Quantitative magnetic resonance imaging (qMRI) derives tissue-specific
parameters -- such as the apparent transverse relaxation rate R2*, the
longitudinal relaxation rate R1 and the magnetisation transfer saturation --
that can be compared across sites and scanners and carry important information
about the underlying microstructure. The multi-parameter mapping (MPM) protocol
takes advantage of multi-echo acquisitions with variable flip angles to extract
these parameters in a clinically acceptable scan time. In this context,
ESTATICS performs a joint loglinear fit of multiple echo series to extract R2*
and multiple extrapolated intercepts, thereby improving robustness to motion
and decreasing the variance of the estimators. In this paper, we extend this
model in two ways: (1) by introducing a joint total variation (JTV) prior on
the intercepts and decay, and (2) by deriving a nonlinear maximum \emph{a
posteriori} estimate. We evaluated the proposed algorithm by predicting
left-out echoes in a rich single-subject dataset. In this validation, we
outperformed other state-of-the-art methods and additionally showed that the
proposed approach greatly reduces the variance of the estimated maps, without
introducing bias.Comment: 11 pages, 2 figures, 1 table, conference paper, accepted at MICCAI
202
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
Fast Fiber Orientation Estimation in Diffusion MRI from kq-Space Sampling and Anatomical Priors
High spatio-angular resolution diffusion MRI (dMRI) has been shown to provide
accurate identification of complex fiber configurations, albeit at the cost of
long acquisition times. We propose a method to recover intra-voxel fiber
configurations at high spatio-angular resolution relying on a kq-space
under-sampling scheme to enable accelerated acquisitions. The inverse problem
for reconstruction of the fiber orientation distribution (FOD) is regularized
by a structured sparsity prior promoting simultaneously voxelwise sparsity and
spatial smoothness of fiber orientation. Prior knowledge of the spatial
distribution of white matter, gray matter and cerebrospinal fluid is also
assumed. A minimization problem is formulated and solved via a forward-backward
convex optimization algorithmic structure. Simulations and real data analysis
suggest that accurate FOD mapping can be achieved from severe kq-space
under-sampling regimes, potentially enabling high spatio-angular dMRI in the
clinical setting.Comment: 10 pages, 5 figures, Supplementary Material
Edge-weighted pFISTA-Net for MRI Reconstruction
Deep learning based on unrolled algorithm has served as an effective method
for accelerated magnetic resonance imaging (MRI). However, many methods ignore
the direct use of edge information to assist MRI reconstruction. In this work,
we present the edge-weighted pFISTA-Net that directly applies the detected edge
map to the soft-thresholding part of pFISTA-Net. The soft-thresholding value of
different regions will be adjusted according to the edge map. Experimental
results of a public brain dataset show that the proposed yields reconstructions
with lower error and better artifact suppression compared with the
state-of-the-art deep learning-based methods. The edge-weighted pFISTA-Net also
shows robustness for different undersampling masks and edge detection
operators. In addition, we extend the edge weighted structure to joint
reconstruction and segmentation network and obtain improved reconstruction
performance and more accurate segmentation results
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