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Shape-aware surface reconstruction from sparse 3D point-clouds Bernard, Florian ; Salamanca Mino, Luis ; Thunberg, Johan et al in Medical Image Analysis (2017), 38 The reconstruction of an object’s shape or surface from a set of 3D points plays an important role in medical image analysis, e.g. in anatomy reconstruction from tomographic measurements or in the process ... [more ▼] The reconstruction of an object’s shape or surface from a set of 3D points plays an important role in medical image analysis, e.g. in anatomy reconstruction from tomographic measurements or in the process of aligning intra-operative navigation and preoperative planning data. In such scenarios, one usually has to deal with sparse data, which significantly aggravates the problem of reconstruction. However, medical applications often provide contextual information about the 3D point data that allow to incorporate prior knowledge about the shape that is to be reconstructed. To this end, we propose the use of a statistical shape model (SSM) as a prior for surface reconstruction. The SSM is represented by a point distribution model (PDM), which is associated with a surface mesh. Using the shape distribution that is modelled by the PDM, we formulate the problem of surface reconstruction from a probabilistic perspective based on a Gaussian Mixture Model (GMM). In order to do so, the given points are interpreted as samples of the GMM. By using mixture components with anisotropic covariances that are “oriented” according to the surface normals at the PDM points, a surface-based fitting is accomplished. Estimating the parameters of the GMM in a maximum a posteriori manner yields the reconstruction of the surface from the given data points. We compare our method to the extensively used Iterative Closest Points method on several different anatomical datasets/SSMs (brain, femur, tibia, hip, liver) and demonstrate superior accuracy and robustness on sparse data. [less ▲] Detailed reference viewed: 194 (21 UL)Enteric neurons from Parkinson's disease patients display ex vivo aberrations in mitochondrial structure. Baumuratov, Aidos ; Antony, Paul ; Ostaszewski, Marek et al in Scientific reports (2016), 6 Based on autopsy material mitochondrial dysfunction has been proposed being part of the pathophysiological cascade of Parkinson's disease (PD). However, in living patients, evidence for such dysfunction ... [more ▼] Based on autopsy material mitochondrial dysfunction has been proposed being part of the pathophysiological cascade of Parkinson's disease (PD). However, in living patients, evidence for such dysfunction is scarce. As the disease presumably starts at the enteric level, we studied ganglionic and mitochondrial morphometrics of enteric neurons. We compared 65 ganglia from 11 PD patients without intestinal symptoms and 41 ganglia from 4 age-matched control subjects. We found that colon ganglia from PD patients had smaller volume, contained significantly more mitochondria per ganglion volume, and displayed a higher total mitochondrial mass relative to controls. This suggests involvement of mitochondrial dysfunction in PD at the enteric level. Moreover, in PD patients the mean mitochondrial volume declined in parallel with motor performance. Ganglionic shrinking was evident in the right but not in the left colon. In contrast, mitochondrial changes prevailed in the left colon suggesting that a compensatory increase in mitochondrial mass might counterbalance mitochondrial dysfunction in the left colon but not in the right colon. Reduction in ganglia volume and combined mitochondrial morphometrics had both predictive power to discriminate between PD patients and control subjects, suggesting that both parameters could be used for early discrimination between PD patients and healthy individuals. [less ▲] Detailed reference viewed: 136 (1 UL)Shape-aware 3D Interpolation using Statistical Shape Models Bernard, Florian ; Salamanca Mino, Luis ; Thunberg, Johan et al in Symposium on Statistical Shape Models and Applications (2015, October) Detailed reference viewed: 166 (36 UL)Improved Parkinson’s disease classification from diffusion MRI data by Fisher vector descriptors Salamanca Mino, Luis ; Vlassis, Nikos ; Diederich, Nico et al in Improved Parkinson’s disease classification from diffusion MRI data by Fisher vector descriptors (2015, October) Due to the complex clinical picture of Parkinson’s disease (PD), the reliable diagnosis of patients is still challenging. A promising approach is the structural characterization of brain areas affected in ... [more ▼] Due to the complex clinical picture of Parkinson’s disease (PD), the reliable diagnosis of patients is still challenging. A promising approach is the structural characterization of brain areas affected in PD by diffusion magnetic resonance imaging (dMRI). Standard classification methods depend on an accurate non-linear alignment of all images to a common reference template, and are challenged by the resulting huge dimensionality of the extracted feature space. Here, we propose a novel diagnosis pipeline based on the Fisher vector algorithm. This technique allows for a precise encoding into a high-level descriptor of standard diffusion measures like the fractional anisotropy and the mean diffusivity, extracted from the regions of interest (ROIs) typically involved in PD. The obtained low dimensional, fixed-length descriptors are independent of the image alignment and boost the linear separability of the problem in the description space, leading to more efficient and accurate diagnosis. In a test cohort of 50 PD patients and 50 controls, the implemented methodology outperforms previous methods when using a logistic linear regressor for classification of each ROI independently, which are subsequently combined into a single classification decision. [less ▲] Detailed reference viewed: 259 (10 UL)Approaching the DT Bound Using Linear Codes in the Short Blocklength Regime Salamanca Mino, Luis ; ; et al in IEEE Communications Letters (2015), 19 The dependence-testing (DT) bound is one of the strongest achievability bounds for the binary erasure channel (BEC) in the finite block length regime. In this paper, we show that maximum likelihood ... [more ▼] The dependence-testing (DT) bound is one of the strongest achievability bounds for the binary erasure channel (BEC) in the finite block length regime. In this paper, we show that maximum likelihood decoded regular low-density parity-check (LDPC) codes with at least 5 ones per column almost achieve the DT bound. Specifically, using quasi-regular LDPC codes with block length of 256 bits, we achieve a rate that is less than 1% away from the rate predicted by the DT bound for a word error rate below 10^−3. The results also indicate that the maximum-likelihood solution is computationally feasible for decoding block codes over the BEC with several hundred bits. [less ▲] Detailed reference viewed: 107 (4 UL)Transitively Consistent and Unbiased Multi-Image Registration Using Numerically Stable Transformation Synchronisation Bernard, Florian ; Thunberg, Johan ; Salamanca Mino, Luis et al in MIDAS Journal (2015) Abstract. Transitive consistency of pairwise transformations is a desir- able property of groupwise image registration procedures. The transfor- mation synchronisation method [4] is able to retrieve ... [more ▼] Abstract. Transitive consistency of pairwise transformations is a desir- able property of groupwise image registration procedures. The transfor- mation synchronisation method [4] is able to retrieve transitively con- sistent pairwise transformations from pairwise transformations that are initially not transitively consistent. In the present paper, we present a numerically stable implementation of the transformation synchronisa- tion method for a ne transformations, which can deal with very large translations, such as those occurring in medical images where the coor- dinate origins may be far away from each other. By using this method in conjunction with any pairwise (a ne) image registration algorithm, a transitively consistent and unbiased groupwise image registration can be achieved. Experiments involving the average template generation from 3D brain images demonstrate that the method is more robust with re- spect to outliers and achieves higher registration accuracy compared to reference-based registration. [less ▲] Detailed reference viewed: 169 (21 UL)Tree expectation propagation for ml decoding of LDPC codes over the BEC Salamanca Mino, Luis ; ; et al in IEEE Transactions on Communications (2013), 61(2), 465-473 We propose a decoding algorithm for LDPC codes that achieves the maximum likelihood (ML) solution over the bi- nary erasure channel (BEC). In this channel, the tree-structured expectation propagation (TEP ... [more ▼] We propose a decoding algorithm for LDPC codes that achieves the maximum likelihood (ML) solution over the bi- nary erasure channel (BEC). In this channel, the tree-structured expectation propagation (TEP) decoder improves the peeling decoder (PD) by processing check nodes of degree one and two. However, it does not achieve the ML solution, as the tree structure of the TEP allows only for approximate inference. In this paper, we provide the procedure to construct the structure needed for exact inference. This algorithm, denoted as generalized tree-structured expectation propagation (GTEP), modifies the code graph by recursively eliminating any check node and merging this information in the remaining graph. The GTEP decoder upon completion either provides the unique ML solution or a tree graph in which the number of parent nodes indicates the multiplicity of the ML solution. We also explain the algorithm as a Gaussian elimination method, relating the GTEP to other ML solutions. Compared to previous approaches, it presents an equivalent complexity, it exhibits a simpler graphical message-passing procedure and, most interesting, the algorithm can be generalized to other channels. [less ▲] Detailed reference viewed: 121 (4 UL)Bayesian equalization for LDPC channel decoding Salamanca Mino, Luis ; ; in IEEE Transactions on Signal Processing (2012), 60(5), 2672-2676 We describe the channel equalization problem, and its prior estimate of the channel state information (CSI), as a joint Bayesian estimation problem to improve each symbol posterior estimates at the input ... [more ▼] We describe the channel equalization problem, and its prior estimate of the channel state information (CSI), as a joint Bayesian estimation problem to improve each symbol posterior estimates at the input of the channel decoder. Our approach takes into consideration not only the uncertainty due to the noise in the channel, but also the uncertainty in the CSI estimate. However, this solution cannot be computed in linear time, because it depends on all the transmitted symbols. Hence, we also put forward an approximation for each symbol's posterior, using the expectation propagation algorithm, which is optimal from the Kullback-Leibler divergence viewpoint and yields an equalization with a complexity identical to the BCJR algorithm. We also use a graphical model representation of the full posterior, in which the proposed approximation can be readily understood. The proposed posterior estimates are more accurate than those computed using the ML estimate for the CSI. In order to illustrate this point, we measure the error rate at the output of a low-density parity-check decoder, which needs the exact posterior for each symbol to detect the incoming word and it is sensitive to a mismatch in those posterior estimates. For example, for QPSK modulation and a channel with three taps, we can expect gains over 0.5 dB with same computational complexity as the ML receiver. [less ▲] Detailed reference viewed: 115 (7 UL) |
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