66 research outputs found
Self Super-Resolution for Magnetic Resonance Images using Deep Networks
High resolution magnetic resonance~(MR) imaging~(MRI) is desirable in many
clinical applications, however, there is a trade-off between resolution, speed
of acquisition, and noise. It is common for MR images to have worse
through-plane resolution~(slice thickness) than in-plane resolution. In these
MRI images, high frequency information in the through-plane direction is not
acquired, and cannot be resolved through interpolation. To address this issue,
super-resolution methods have been developed to enhance spatial resolution. As
an ill-posed problem, state-of-the-art super-resolution methods rely on the
presence of external/training atlases to learn the transform from low
resolution~(LR) images to high resolution~(HR) images. For several reasons,
such HR atlas images are often not available for MRI sequences. This paper
presents a self super-resolution~(SSR) algorithm, which does not use any
external atlas images, yet can still resolve HR images only reliant on the
acquired LR image. We use a blurred version of the input image to create
training data for a state-of-the-art super-resolution deep network. The trained
network is applied to the original input image to estimate the HR image. Our
SSR result shows a significant improvement on through-plane resolution compared
to competing SSR methods.Comment: Accepted by IEEE International Symposium on Biomedical Imaging (ISBI)
201
On Finite Difference Jacobian Computation in Deformable Image Registration
Producing spatial transformations that are diffeomorphic has been a central
problem in deformable image registration. As a diffeomorphic transformation
should have positive Jacobian determinant everywhere, the number of
voxels with has been used to test for diffeomorphism and also to
measure the irregularity of the transformation. For digital transformations,
is commonly approximated using central difference, but this strategy can
yield positive 's for transformations that are clearly not diffeomorphic
-- even at the voxel resolution level. To show this, we first investigate the
geometric meaning of different finite difference approximations of . We
show that to determine diffeomorphism for digital images, use of any individual
finite difference approximations of is insufficient. We show that for a
2D transformation, four unique finite difference approximations of 's must
be positive to ensure the entire domain is invertible and free of folding at
the pixel level. We also show that in 3D, ten unique finite differences
approximations of 's are required to be positive. Our proposed digital
diffeomorphism criteria solves several errors inherent in the central
difference approximation of and accurately detects non-diffeomorphic
digital transformations
Coordinate Translator for Learning Deformable Medical Image Registration
The majority of deep learning (DL) based deformable image registration
methods use convolutional neural networks (CNNs) to estimate displacement
fields from pairs of moving and fixed images. This, however, requires the
convolutional kernels in the CNN to not only extract intensity features from
the inputs but also understand image coordinate systems. We argue that the
latter task is challenging for traditional CNNs, limiting their performance in
registration tasks. To tackle this problem, we first introduce Coordinate
Translator, a differentiable module that identifies matched features between
the fixed and moving image and outputs their coordinate correspondences without
the need for training. It unloads the burden of understanding image coordinate
systems for CNNs, allowing them to focus on feature extraction. We then propose
a novel deformable registration network, im2grid, that uses multiple Coordinate
Translator's with the hierarchical features extracted from a CNN encoder and
outputs a deformation field in a coarse-to-fine fashion. We compared im2grid
with the state-of-the-art DL and non-DL methods for unsupervised 3D magnetic
resonance image registration. Our experiments show that im2grid outperforms
these methods both qualitatively and quantitatively
Optimal operating MR contrast for brain ventricle parcellation
Development of MR harmonization has enabled different contrast MRIs to be
synthesized while preserving the underlying anatomy. In this paper, we use
image harmonization to explore the impact of different T1-w MR contrasts on a
state-of-the-art ventricle parcellation algorithm VParNet. We identify an
optimal operating contrast (OOC) for ventricle parcellation; by showing that
the performance of a pretrained VParNet can be boosted by adjusting contrast to
the OOC
Intensity Inhomogeneity Correction of SD-OCT Data Using Macular Flatspace
Images of the retina acquired using optical coherence tomography (OCT) often suffer from intensity inhomogeneity problems that degrade both the quality of the images and the performance of automated algorithms utilized to measure structural changes. This intensity variation has many causes, including off-axis acquisition, signal attenuation, multi-frame averaging, and vignetting, making it difficult to correct the data in a fundamental way. This paper presents a method for inhomogeneity correction by acting to reduce the variability of intensities within each layer. In particular, the N3 algorithm, which is popular in neuroimage analysis, is adapted to work for OCT data. N3 works by sharpening the intensity histogram, which reduces the variation of intensities within different classes. To apply it here, the data are first converted to a standardized space called macular flat space (MFS). MFS allows the intensities within each layer to be more easily normalized by removing the natural curvature of the retina. N3 is then run on the MFS data using a modified smoothing model, which improves the efficiency of the original algorithm. We show that our method more accurately corrects gain fields on synthetic OCT data when compared to running N3 on non-flattened data. It also reduces the overall variability of the intensities within each layer, without sacrificing contrast between layers, and improves the performance of registration between OCT images
A Survey on Deep Learning in Medical Image Registration: New Technologies, Uncertainty, Evaluation Metrics, and Beyond
Over the past decade, deep learning technologies have greatly advanced the
field of medical image registration. The initial developments, such as
ResNet-based and U-Net-based networks, laid the groundwork for deep
learning-driven image registration. Subsequent progress has been made in
various aspects of deep learning-based registration, including similarity
measures, deformation regularizations, and uncertainty estimation. These
advancements have not only enriched the field of deformable image registration
but have also facilitated its application in a wide range of tasks, including
atlas construction, multi-atlas segmentation, motion estimation, and 2D-3D
registration. In this paper, we present a comprehensive overview of the most
recent advancements in deep learning-based image registration. We begin with a
concise introduction to the core concepts of deep learning-based image
registration. Then, we delve into innovative network architectures, loss
functions specific to registration, and methods for estimating registration
uncertainty. Additionally, this paper explores appropriate evaluation metrics
for assessing the performance of deep learning models in registration tasks.
Finally, we highlight the practical applications of these novel techniques in
medical imaging and discuss the future prospects of deep learning-based image
registration
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