9,617 research outputs found
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
Robust Machine Learning-Based Correction on Automatic Segmentation of the Cerebellum and Brainstem.
Automated segmentation is a useful method for studying large brain structures such as the cerebellum and brainstem. However, automated segmentation may lead to inaccuracy and/or undesirable boundary. The goal of the present study was to investigate whether SegAdapter, a machine learning-based method, is useful for automatically correcting large segmentation errors and disagreement in anatomical definition. We further assessed the robustness of the method in handling size of training set, differences in head coil usage, and amount of brain atrophy. High resolution T1-weighted images were acquired from 30 healthy controls scanned with either an 8-channel or 32-channel head coil. Ten patients, who suffered from brain atrophy because of fragile X-associated tremor/ataxia syndrome, were scanned using the 32-channel head coil. The initial segmentations of the cerebellum and brainstem were generated automatically using Freesurfer. Subsequently, Freesurfer's segmentations were both manually corrected to serve as the gold standard and automatically corrected by SegAdapter. Using only 5 scans in the training set, spatial overlap with manual segmentation in Dice coefficient improved significantly from 0.956 (for Freesurfer segmentation) to 0.978 (for SegAdapter-corrected segmentation) for the cerebellum and from 0.821 to 0.954 for the brainstem. Reducing the training set size to 2 scans only decreased the Dice coefficient ≤0.002 for the cerebellum and ≤ 0.005 for the brainstem compared to the use of training set size of 5 scans in corrective learning. The method was also robust in handling differences between the training set and the test set in head coil usage and the amount of brain atrophy, which reduced spatial overlap only by <0.01. These results suggest that the combination of automated segmentation and corrective learning provides a valuable method for accurate and efficient segmentation of the cerebellum and brainstem, particularly in large-scale neuroimaging studies, and potentially for segmenting other neural regions as well
Heavy Ion Physics at the LHC with the ATLAS Detector
The ATLAS detector at CERN will provide a high-resolution
longitudinally-segmented calorimeter and precision tracking for the upcoming
study of heavy ion collisions at the LHC (sqrt(s_NN)=5520 GeV). The calorimeter
covers |eta|<5 with both electromagnetic and hadronic sections, while the inner
detector spectrometer covers |eta|<2.5. ATLAS will study a full range of
observables necessary to characterize the hot and dense matter formed at the
LHC. Global measurements (particle multiplicities, collective flow) will
provide access into its thermodynamic and hydrodynamic properties. Measuring
complete jets out to 100's of GeV will allow detailed studies of energy loss
and its effect on jets. Quarkonia will provide a handle on deconfinement
mechanisms. ATLAS will also study the structure of the nucleon and nucleus
using forward physics probes and ultraperipheral collisions, both enabled by
segmented Zero Degree Calorimeters.Comment: 9 pages, 8 figures, submitted to the Proceedings of Quark Matter
2006, Shanghai, China, November 14-20, 200
Attenuation correction for brain PET imaging using deep neural network based on dixon and ZTE MR images
Positron Emission Tomography (PET) is a functional imaging modality widely
used in neuroscience studies. To obtain meaningful quantitative results from
PET images, attenuation correction is necessary during image reconstruction.
For PET/MR hybrid systems, PET attenuation is challenging as Magnetic Resonance
(MR) images do not reflect attenuation coefficients directly. To address this
issue, we present deep neural network methods to derive the continuous
attenuation coefficients for brain PET imaging from MR images. With only Dixon
MR images as the network input, the existing U-net structure was adopted and
analysis using forty patient data sets shows it is superior than other Dixon
based methods. When both Dixon and zero echo time (ZTE) images are available,
we have proposed a modified U-net structure, named GroupU-net, to efficiently
make use of both Dixon and ZTE information through group convolution modules
when the network goes deeper. Quantitative analysis based on fourteen real
patient data sets demonstrates that both network approaches can perform better
than the standard methods, and the proposed network structure can further
reduce the PET quantification error compared to the U-net structure.Comment: 15 pages, 12 figure
Robust point correspondence applied to two and three-dimensional image registration
Accurate and robust correspondence calculations are very important in many medical and biological applications. Often, the correspondence calculation forms part of a rigid registration algorithm, but accurate correspondences are especially important for elastic registration algorithms and for quantifying changes over time. In this paper, a new correspondence calculation algorithm, CSM (correspondence by sensitivity to movement), is described. A robust corresponding point is calculated by determining the sensitivity of a correspondence to movement of the point being matched. If the correspondence is reliable, a perturbation in the position of this point should not result in a large movement of the correspondence. A measure of reliability is also calculated. This correspondence calculation method is independent of the registration transformation and has been incorporated into both a 2D elastic registration algorithm for warping serial sections and a 3D rigid registration algorithm for registering pre and postoperative facial range scans. These applications use different methods for calculating the registration transformation and accurate rigid and elastic alignment of images has been achieved with the CSM method. It is expected that this method will be applicable to many different applications and that good results would be achieved if it were to be inserted into other methods for calculating a registration transformation from correspondence
Predicting Slice-to-Volume Transformation in Presence of Arbitrary Subject Motion
This paper aims to solve a fundamental problem in intensity-based 2D/3D
registration, which concerns the limited capture range and need for very good
initialization of state-of-the-art image registration methods. We propose a
regression approach that learns to predict rotation and translations of
arbitrary 2D image slices from 3D volumes, with respect to a learned canonical
atlas co-ordinate system. To this end, we utilize Convolutional Neural Networks
(CNNs) to learn the highly complex regression function that maps 2D image
slices into their correct position and orientation in 3D space. Our approach is
attractive in challenging imaging scenarios, where significant subject motion
complicates reconstruction performance of 3D volumes from 2D slice data. We
extensively evaluate the effectiveness of our approach quantitatively on
simulated MRI brain data with extreme random motion. We further demonstrate
qualitative results on fetal MRI where our method is integrated into a full
reconstruction and motion compensation pipeline. With our CNN regression
approach we obtain an average prediction error of 7mm on simulated data, and
convincing reconstruction quality of images of very young fetuses where
previous methods fail. We further discuss applications to Computed Tomography
and X-ray projections. Our approach is a general solution to the 2D/3D
initialization problem. It is computationally efficient, with prediction times
per slice of a few milliseconds, making it suitable for real-time scenarios.Comment: 8 pages, 4 figures, 6 pages supplemental material, currently under
review for MICCAI 201
MinMax Radon Barcodes for Medical Image Retrieval
Content-based medical image retrieval can support diagnostic decisions by
clinical experts. Examining similar images may provide clues to the expert to
remove uncertainties in his/her final diagnosis. Beyond conventional feature
descriptors, binary features in different ways have been recently proposed to
encode the image content. A recent proposal is "Radon barcodes" that employ
binarized Radon projections to tag/annotate medical images with content-based
binary vectors, called barcodes. In this paper, MinMax Radon barcodes are
introduced which are superior to "local thresholding" scheme suggested in the
literature. Using IRMA dataset with 14,410 x-ray images from 193 different
classes, the advantage of using MinMax Radon barcodes over \emph{thresholded}
Radon barcodes are demonstrated. The retrieval error for direct search drops by
more than 15\%. As well, SURF, as a well-established non-binary approach, and
BRISK, as a recent binary method are examined to compare their results with
MinMax Radon barcodes when retrieving images from IRMA dataset. The results
demonstrate that MinMax Radon barcodes are faster and more accurate when
applied on IRMA images.Comment: To appear in proceedings of the 12th International Symposium on
Visual Computing, December 12-14, 2016, Las Vegas, Nevada, US
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