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Chapter and Conference Paper
Over-and-Under Complete Convolutional RNN for MRI Reconstruction
Reconstructing magnetic resonance (MR) images from under-sampled data is a challenging problem due to various artifacts introduced by the under-sampling operation. Recent deep learning-based methods for MR ima...
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Chapter and Conference Paper
Hydranet: Data Augmentation for Regression Neural Networks
Deep learning techniques are often criticized to heavily depend on a large quantity of labeled data. This problem is even more challenging in medical image analysis where the annotator expertise is often scar...
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Chapter and Conference Paper
Generative Adversarial Network for Segmentation of Motion Affected Neonatal Brain MRI
Automatic neonatal brain tissue segmentation in preterm born infants is a prerequisite for evaluation of brain development. However, automatic segmentation is often hampered by motion artifacts caused by infan...
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Chapter and Conference Paper
Multiple Sclerosis Lesion Segmentation with Tiramisu and 2.5D Stacked Slices
In this paper, we present a fully convolutional densely connected network (Tiramisu) for multiple sclerosis (MS) lesion segmentation. Different from existing methods, we use stacked slices from all three anato...
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Chapter and Conference Paper
Optimal Experimental Design for Biophysical Modelling in Multidimensional Diffusion MRI
Computational models of biophysical tissue properties have been widely used in diffusion MRI (dMRI) research to elucidate the link between microstructural properties and MR signal formation. For brain tissue,...
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Chapter and Conference Paper
Automated Lesion Detection by Regressing Intensity-Based Distance with a Neural Network
Localization of focal vascular lesions on brain MRI is an important component of research on the etiology of neurological disorders. However, manual annotation of lesions can be challenging, time-consuming an...
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Chapter and Conference Paper
Variational AutoEncoder for Regression: Application to Brain Aging Analysis
While unsupervised variational autoencoders (VAE) have become a powerful tool in neuroimage analysis, their application to supervised learning is under-explored. We aim to close this gap by proposing a unified...
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Chapter and Conference Paper
Automatic Paraspinal Muscle Segmentation in Patients with Lumbar Pathology Using Deep Convolutional Neural Network
Recent evidence suggests an association between low back pain (LBP) and changes in lumbar paraspinal muscle morphology and composition (i.e., fatty infiltration). Quantitative measurements of muscle cross-sect...
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Chapter and Conference Paper
Building an Ensemble of Complementary Segmentation Methods by Exploiting Probabilistic Estimates
Two common ways of approaching atlas-based segmentation of brain MRI are (1) intensity-based modelling and (2) multi-atlas label fusion. Intensity-based methods are robust to registration errors but need disti...
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Chapter and Conference Paper
Photoacoustic Imaging Paradigm Shift: Towards Using Vendor-Independent Ultrasound Scanners
Photoacoustic (PA) imaging requires channel data acquisition synchronized with a laser firing system. Unfortunately, the access to these channel data is only available on specialized research systems, and most...
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Chapter and Conference Paper
Class-Driven Color Transformation for Semantic Labeling
We propose a novel class-driven color transformation aimed at semantic labeling. In contrast with other approaches elsewhere in the literature, our approach is a supervised one employing class information to l...
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Chapter and Conference Paper
Element Stiffness Matrix Integration in Image-Based Cartesian Grid Finite Element Method
Patient specific Finite Element (FE) simulations are usually expensive. Time consuming geometry creation procedures are normally necessary to use standard FE meshing software, while direct pixel-based meshing ...
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Chapter and Conference Paper
Estimating Anatomically-Correct Reference Model for Craniomaxillofacial Deformity via Sparse Representation
The success of craniomaxillofacial (CMF) surgery depends not only on the surgical techniques, but also upon an accurate surgical planning. However, surgical planning for CMF surgery is challenging due to the a...
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Chapter and Conference Paper
Active Echo: A New Paradigm for Ultrasound Calibration
In ultrasound-guided medical procedures, accurate tracking of interventional tools with respect to the US probe is crucial to patient safety and clinical outcome. US probe tracking requires an unavoidable cali...
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Chapter and Conference Paper
A Computer Assisted Planning System for the Placement of sEEG Electrodes in the Treatment of Epilepsy
Approximately 20–30% of patients with focal epilepsy are medically refractory and may be candidates for curative surgery. Stereo EEG is the placement of multiple depth electrodes into the brain to record seizu...
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Chapter and Conference Paper
Network-Guided Group Feature Selection for Classification of Autism Spectrum Disorder
We present an anatomically guided feature selection scheme for prediction of neurological disorders based on brain connectivity networks. Using anatomical information not only gives rise to an interpretable mo...
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Chapter and Conference Paper
Matched Signal Detection on Graphs: Theory and Application to Brain Network Classification
We develop a matched signal detection (MSD) theory for signals with an intrinsic structure described by a weighted graph. Hypothesis tests are formulated under different signal models. In the simplest scenario...
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Chapter and Conference Paper
Hierarchical Structural Map** for Globally Optimized Estimation of Functional Networks
In this study, we propose a framework to map functional MRI (fMRI) activation signals using DTI-tractography. This framework, which we term functional by structural hierarchical (FSH) map**, models the regio...
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Chapter and Conference Paper
Direct 3D Ultrasound to Video Registration Using Photoacoustic Effect
Interventional guidance systems require surgical navigation systems to register different tools and devices together. Standard navigation systems have various drawbacks leading to target registration errors (T...
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Chapter and Conference Paper
Amygdala Surface Modeling with Weighted Spherical Harmonics
Although there are numerous publications on amygdala volumetry, so far there has not been many studies on modeling local amygdala surface shape variations in a rigorous framework. This paper present a systemat...