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		<title><![CDATA[ Medical Imaging, IEEE Transactions on - new TOC ]]></title>
		<link>http://ieeexplore.ieee.org</link>
		<description>TOC Alert for Publication# 42 </description>
		<year>2012</year>
		<month>February </month>
		<day>10</day>
		<item>
			<title><![CDATA[Table of Contents]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6142690]]></link>
			<description><![CDATA[ ]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6142690]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>C1</startPage>
			<endPage>C4</endPage>
			<fileSize>115</fileSize>
			<authors><![CDATA[]]></authors>
		</item>
		<item>
			<title><![CDATA[IEEE Transactions on Medical Imaging publication information]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6142691]]></link>
			<description><![CDATA[ ]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6142691]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>C2</startPage>
			<endPage>C2</endPage>
			<fileSize>43</fileSize>
			<authors><![CDATA[]]></authors>
		</item>
		<item>
			<title><![CDATA[Image Similarity and Tissue Overlaps as Surrogates for Image Registration Accuracy: Widely Used but Unreliable]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=5977031]]></link>
			<description><![CDATA[The accuracy of nonrigid image registrations is commonly approximated using surrogate measures such as tissue label overlap scores, image similarity, image difference, or transformation inverse consistency error. This paper provides experimental evidence that these measures, even when used in combination, cannot distinguish accurate from inaccurate registrations. To this end, we introduce a &#x201C;registration&#x201D; algorithm that generates highly inaccurate image transformations, yet performs extremely well in terms of the surrogate measures. Of the tested criteria, only overlap scores of localized anatomical regions reliably distinguish reasonable from inaccurate registrations, whereas image similarity and tissue overlap do not. We conclude that tissue overlap and image similarity, whether used alone or together, do not provide valid evidence for accurate registrations and should thus not be reported or accepted as such.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=5977031]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>153</startPage>
			<endPage>163</endPage>
			<fileSize>2313</fileSize>
			<authors><![CDATA[Rohlfing, T.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Joint Modeling of Anatomical and Functional Connectivity for Population Studies]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=5999719]]></link>
			<description><![CDATA[We propose a novel probabilistic framework to merge information from diffusion weighted imaging tractography and resting-state functional magnetic resonance imaging correlations to identify connectivity patterns in the brain. In particular, we model the interaction between latent anatomical and functional connectivity and present an intuitive extension to population studies. We employ the EM algorithm to estimate the model parameters by maximizing the data likelihood. The method simultaneously infers the templates of latent connectivity for each population and the differences in connectivity between the groups. We demonstrate our method on a schizophrenia study. Our model identifies significant increases in functional connectivity between the parietal/posterior cingulate region and the frontal lobe and reduced functional connectivity between the parietal/posterior cingulate region and the temporal lobe in schizophrenia. We further establish that our model learns predictive differences between the control and clinical populations, and that combining the two modalities yields better results than considering each one in isolation.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=5999719]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>164</startPage>
			<endPage>182</endPage>
			<fileSize>2633</fileSize>
			<authors><![CDATA[Venkataraman, A.;Rathi, Y.;Kubicki, M.;Westin, C.-F.;Golland, P.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Multi-Channel Microstrip Transceiver Arrays Using Harmonics for High Field MR Imaging in Humans]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6003790]]></link>
			<description><![CDATA[Radio-frequency (RF) transceiver array design using primary and higher order harmonics for in vivo parallel magnetic resonance imaging imaging (MRI) and spectroscopic imaging is proposed. The improved electromagnetic decoupling performance, unique magnetic field distributions and high-frequency operation capabilities of higher-order harmonics of resonators would benefit transceiver arrays for parallel MRI, especially for ultrahigh field parallel MRI. To demonstrate this technique, microstrip transceiver arrays using first and second harmonic resonators were developed for human head parallel imaging at 7T. Phantom and human head images were acquired and evaluated using the GRAPPA reconstruction algorithm. The higher-order harmonic transceiver array design technique was also assessed numerically using FDTD simulation. Compared with regular primary-resonance transceiver designs, the proposed higher-order harmonic technique provided an improved g-factor and increased decoupling among resonant elements without using dedicated decoupling circuits, which would potentially lead to a better parallel imaging performance and ultimately faster and higher quality imaging. The proposed technique is particularly suitable for densely spaced transceiver array design where the increased mutual inductance among the elements becomes problematic. In addition, it also provides a simple approach to readily upgrade the channels of a conventional primary resonator microstrip array to a larger number for faster imaging.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6003790]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>183</startPage>
			<endPage>191</endPage>
			<fileSize>1565</fileSize>
			<authors><![CDATA[Wu, B.;Wang, C.;Lu, J.;Pang, Y.;Nelson, S. J.;Vigneron, D. B.;Zhang, X.;]]></authors>
		</item>
		<item>
			<title><![CDATA[HRF Estimation in fMRI Data With an Unknown Drift Matrix by Iterative Minimization of the Kullback&#x2013;Leibler Divergence]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6011702]]></link>
			<description><![CDATA[Hemodynamic response function (HRF) estimation in noisy functional magnetic resonance imaging (fMRI) plays an important role when investigating the temporal dynamic of a brain region response during activations. Nonparametric methods which allow more flexibility in the estimation by inferring the HRF at each time sample have provided improved performance in comparison to the parametric methods. In this paper, the mixed-effects model is used to derive a new algorithm for nonparametric maximum likelihood HRF estimation. In this model, the random effect is used to better account for the variability of the drift. Contrary to the usual approaches, the proposed algorithm has the benefit of considering an unknown and therefore flexible drift matrix. This allows the effective representation of a broader class of drift signals and therefore the reduction of the error in approximating the drift component. Estimates of the HRF and the hyperparameters are derived by iterative minimization of the Kullback&#x2013;Leibler divergence between a model family of probability distributions defined using the mixed-effects model and a desired family of probability distributions constrained to be concentrated on the observed data. The performance of proposed method is demonstrated on simulated and real fMRI data, the latter originating from both event-related and block design fMRI experiments.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6011702]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>192</startPage>
			<endPage>206</endPage>
			<fileSize>1900</fileSize>
			<authors><![CDATA[Seghouane, A.-K.;Shah, A.;]]></authors>
		</item>
		<item>
			<title><![CDATA[NMF-SVM Based CAD Tool Applied to Functional Brain Images for the Diagnosis of Alzheimer's Disease]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6017128]]></link>
			<description><![CDATA[This paper presents a novel computer-aided diagnosis (CAD) technique for the early diagnosis of the Alzheimer's disease (AD) based on nonnegative matrix factorization (NMF) and support vector machines (SVM) with bounds of confidence. The CAD tool is designed for the study and classification of functional brain images. For this purpose, two different brain image databases are selected: a single photon emission computed tomography (SPECT) database and positron emission tomography (PET) images, both of them containing data for both Alzheimer's disease (AD) patients and healthy controls as a reference. These databases are analyzed by applying the Fisher discriminant ratio (FDR) and nonnegative matrix factorization (NMF) for feature selection and extraction of the most relevant features. The resulting NMF-transformed sets of data, which contain a reduced number of features, are classified by means of a SVM-based classifier with bounds of confidence for decision. The proposed NMF-SVM method yields up to 91% classification accuracy with high sensitivity and specificity rates (upper than 90%). This NMF-SVM CAD tool becomes an accurate method for SPECT and PET AD image classification.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6017128]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>207</startPage>
			<endPage>216</endPage>
			<fileSize>921</fileSize>
			<authors><![CDATA[Padilla, P.;Lopez, M.;Gorriz, J. M.;Ramirez, J.;Salas-Gonzalez, D.;Alvarez, I.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Fasciculography: Robust Prior-Free Real-Time Normalized Volumetric Neural Tract Parcellation]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6017127]]></link>
			<description><![CDATA[Fiber tracking in diffusion tensor magnetic resonance images (DTIs) reveals 3-D structural connectivity of the brain conveniently and thus is a viable tool for investigating neural differences. Unfortunately, local noise, image artifacts and numerical tracking errors during integration-based techniques are cumulative. Prematurely terminated fibers and under-sampled fiber bundles result in incomplete reconstruction of white matter fiber tracts and hence incorrect anatomical measurements. Quantitative cross-subject tract analysis, which is critical for abnormality detection, is complicated by inefficient and inaccurate tract reconstruction and normalization from fiber bundles. Because of the above problems, we propose a parcellation method that aims for lower sensitivity to initialization and local orientation error by directly segmenting full white matter tracts (Fasciculography), rather than reconstructing individual curves, from diffusion tensor fields. A fast, robust volumetric, and intrinsically normalized solution is achieved by noise-filtering using a generic parametrized tract model to prevent premature tract termination. At the same time, orientation information reduces the search space, significantly speeding up the tract parcellation process with less human intervention. Detailed comparisons against streamline tracking, shortest-path tracking, and nonrigid registration using synthetic and real DTIs confirmed the superior properties of Fasciculography. Since a normalized tract can be delineated interactively in a just few seconds using the proposed method, accurate high volume tract comparisons become feasible.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6017127]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>217</startPage>
			<endPage>230</endPage>
			<fileSize>1605</fileSize>
			<authors><![CDATA[Ho, H. P.;Wang, F.;Papademetris, X.;Blumberg, H. P.;Staib, L. H.;]]></authors>
		</item>
		<item>
			<title><![CDATA[A Function for Quality Evaluation of Retinal Vessel Segmentations]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6019055]]></link>
			<description><![CDATA[Retinal blood vessel assessment plays an important role in the diagnosis of ophthalmic pathologies. The use of digital images for this purpose enables the application of a computerized approach and has fostered the development of multiple methods for automated vascular tree segmentation. Metrics based on contingency tables for binary classification have been widely used for evaluating the performance of these algorithms. Metrics from this family are based on the measurement of a success or failure rate in the detected pixels, obtained by means of pixel-to-pixel comparison between the automated segmentation and a manually-labeled reference image. Therefore, vessel pixels are not considered as a part of a vascular structure with specific features. This paper contributes a function for the evaluation of global quality in retinal vessel segmentations. This function is based on the characterization of vascular structures as connected segments with measurable area and length. Thus, its design is meant to be sensitive to anatomical vascularity features. Comparison of results between the proposed function and other general quality evaluation functions shows that this proposal renders a high matching degree with human quality perception. Therefore, it can be used to enhance quality evaluation in retinal vessel segmentations, supplementing the existing functions. On the other hand, from a general point of view, the applied concept of measuring descriptive properties may be used to design specialized functions aimed at segmentation quality evaluation in other complex structures.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6019055]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>231</startPage>
			<endPage>239</endPage>
			<fileSize>908</fileSize>
			<authors><![CDATA[Gegundez-Arias, M. E.;Aquino, A.;Bravo, J. M.;Marin, D.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Automatic Detection and Segmentation of Lymph Nodes From CT Data]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6033061]]></link>
			<description><![CDATA[Lymph nodes are assessed routinely in clinical practice and their size is followed throughout radiation or chemotherapy to monitor the effectiveness of cancer treatment. This paper presents a robust learning-based method for automatic detection and segmentation of solid lymph nodes from CT data, with the following contributions. First, it presents a learning based approach to solid lymph node detection that relies on marginal space learning to achieve great speedup with virtually no loss in accuracy. Second, it presents a computationally efficient segmentation method for solid lymph nodes (LN). Third, it introduces two new sets of features that are effective for LN detection, one that self-aligns to high gradients and another set obtained from the segmentation result. The method is evaluated for axillary LN detection on 131 volumes containing 371 LN, yielding a 83.0% detection rate with 1.0 false positive per volume. It is further evaluated for pelvic and abdominal LN detection on 54 volumes containing 569 LN, yielding a 80.0% detection rate with 3.2 false positives per volume. The running time is 5&#x2013;20 s per volume for axillary areas and 15&#x2013;40 s for pelvic. An added benefit of the method is the capability to detect and segment conglomerated lymph nodes.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6033061]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>240</startPage>
			<endPage>250</endPage>
			<fileSize>1501</fileSize>
			<authors><![CDATA[Barbu, A.;Suehling, M.;Xu, X.;Liu, D.;Zhou, S. K.;Comaniciu, D.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Brain Surface Conformal Parameterization With the Ricci Flow]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6020804]]></link>
			<description><![CDATA[In brain mapping research, parameterized 3-D surface models are of great interest for statistical comparisons of anatomy, surface-based registration, and signal processing. Here, we introduce the theories of continuous and discrete surface Ricci flow, which can create Riemannian metrics on surfaces with arbitrary topologies with user-defined Gaussian curvatures. The resulting conformal parameterizations have no singularities and they are intrinsic and stable. First, we convert a cortical surface model into a multiple boundary surface by cutting along selected anatomical landmark curves. Secondly, we conformally parameterize each cortical surface to a parameter domain with a user-designed Gaussian curvature arrangement. In the parameter domain, a shape index based on conformal invariants is computed, and inter-subject cortical surface matching is performed by solving a constrained harmonic map. We illustrate various target curvature arrangements and demonstrate the stability of the method using longitudinal data. To map statistical differences in cortical morphometry, we studied brain asymmetry in 14 healthy control subjects. We used a manifold version of Hotelling's <formula formulatype="inline"><tex Notation="TeX">$T^{2}$</tex> </formula> test, applied to the Jacobian matrices of the surface parameterizations. A permutation test, along with the cumulative distribution of <formula formulatype="inline"> <tex Notation="TeX">$p$</tex></formula>-values, were used to estimate the overall statistical significance of differences. The results show our algorithm's power to detect subtle group differences in cortical surfaces.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6020804]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>251</startPage>
			<endPage>264</endPage>
			<fileSize>895</fileSize>
			<authors><![CDATA[Wang, Y.;Shi, J.;Yin, X.;Gu, X.;Chan, T. F.;Yau, S.-T.;Toga, A. W.;Thompson, P. M.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Generating Super Stimulated-Echoes in MRI and Their Application to Hyperpolarized C-13 Diffusion Metabolic Imaging]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6058659]]></link>
			<description><![CDATA[Stimulated-echoes in MR can be used to provide high sensitivity to motion and flow, creating diffusion and perfusion weighting as well as <formula formulatype="inline"><tex Notation="TeX">$T_{1}$</tex></formula> contrast, but conventional approaches inherently suffer from a 50% signal loss. The super stimulated-echo, which uses a specialized radio-frequency (RF) pulse train, has been proposed in order to improve the signal while preserving motion and <formula formulatype="inline"><tex Notation="TeX">$T_{1}$</tex></formula> sensitivity. This paper presents a novel and straightforward method for designing the super stimulated-echo pulse train using inversion pulse design techniques. This method can also create adiabatic designs with an improved response to RF transmit field variations. The scheme was validated in phantom experiments and shown in vivo to improve signal-to-noise ratio (SNR). We have applied a super stimulated-echo to metabolic MRI with hyperpolarized <formula formulatype="inline"><tex Notation="TeX">$^{13}{rm C}$</tex></formula>-labeled molecules. For spectroscopic imaging of hyperpolarized agents, several repetition times are required but only a single stimulated-echo encoding is feasible, which can lead to unwanted motion blurring. To address this, a super stimulated-echo preparation scheme was used in which the diffusion weighting is terminated prior to the acquisition, and we observed a SNR increases of 60% in phantoms and 49% in vivo over a conventional stimulated-echo. Experiments following injection of hyperpolarized <formula formulatype="inline"><tex Notation="TeX">$[1{hbox{-}}^{13}{rm C}]$</tex> </formula>-pyruvate in murine transgenic cancer models have shown improved delineation for tumors since signals from metabolites within tumor tissues are retained while those from the vasculature are suppressed by the diffusion preparation scheme.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6058659]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>265</startPage>
			<endPage>275</endPage>
			<fileSize>1202</fileSize>
			<authors><![CDATA[Larson, P. E. Z.;Kerr, A. B.;Reed, G. D.;Hurd, R. E.;Kurhanewicz, J.;Pauly, J. M.;Vigneron, D. B.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Automated Brain Structure Segmentation Based on Atlas Registration and Appearance Models]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6021414]]></link>
			<description><![CDATA[Accurate automated brain structure segmentation methods facilitate the analysis of large-scale neuroimaging studies. This work describes a novel method for brain structure segmentation in magnetic resonance images that combines information about a structure's location and appearance. The spatial model is implemented by registering multiple atlas images to the target image and creating a spatial probability map. The structure's appearance is modeled by a classifier based on Gaussian scale-space features. These components are combined with a regularization term in a Bayesian framework that is globally optimized using graph cuts. The incorporation of the appearance model enables the method to segment structures with complex intensity distributions and increases its robustness against errors in the spatial model. The method is tested in cross-validation experiments on two datasets acquired with different magnetic resonance sequences, in which the hippocampus and cerebellum were segmented by an expert. Furthermore, the method is compared to two other segmentation techniques that were applied to the same data. Results show that the atlas- and appearance-based method produces accurate results with mean Dice similarity indices of 0.95 for the cerebellum, and 0.87 for the hippocampus. This was comparable to or better than the other methods, whereas the proposed technique is more widely applicable and robust.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6021414]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>276</startPage>
			<endPage>286</endPage>
			<fileSize>1050</fileSize>
			<authors><![CDATA[van der Lijn, F.;de Bruijne, M.;Klein, S.;den Heijer, T.;Hoogendam, Y. Y.;van der Lugt, A.;Breteler, M. M. B.;Niessen, W. J.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Reference-Free PRFS MR-Thermometry Using Near-Harmonic 2-D Reconstruction of the Background Phase]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6021375]]></link>
			<description><![CDATA[Proton resonance frequency shift (PRFS) MR thermometry (MRT) is the generally preferred method for monitoring thermal ablation, typically implemented with gradient-echo (GRE) sequences. Standard PRFS MRT is based on the subtraction of a temporal reference phase map and is, therefore, intrinsically sensitive to tissue motion (including deformation) and to external perturbation of the magnetic field. Reference-free (or reference-less) PRFS MRT has been previously described by Rieke <etal/> and was based on a 2-D polynomial fit performed on phase data from outside the heated region, to estimate the background phase inside the region of interest. While their approach was undeniably a fundamental progress in terms of robustness against tissue motion and magnetic perturbations, the underlying mathematical formalism requires a thick unheated border and may be subject to numerical instabilities with high order polynomials. A novel method of reference-free PRFS MRT is described here, using a physically consistent formalism, which exploits mathematical properties of the magnetic field in a homogeneous or near-homogeneous medium.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6021375]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>287</startPage>
			<endPage>301</endPage>
			<fileSize>3265</fileSize>
			<authors><![CDATA[Salomir, R.;Viallon, M.;Kickhefel, A.;Roland, J.;Morel, D. R.;Petrusca, L.;Auboiroux, V.;Goget, T.;Terraz, S.;Becker, C. D.;Gross, P.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Principal Component Based Diffeomorphic Surface Mapping]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6022802]]></link>
			<description><![CDATA[We present a new diffeomorphic surface mapping algorithm under the framework of large deformation diffeomorphic metric mapping (LDDMM). Unlike existing LDDMM approaches, this new algorithm reduces the complexity of the estimation of diffeomorphic transformations by incorporating a shape prior in which a nonlinear diffeomorphic shape space is represented by a linear space of initial momenta of diffeomorphic geodesic flows from a fixed template. In addition, for the first time, the diffeomorphic mapping is formulated within a decision-theoretic scheme based on Bayesian modeling in which an empirical shape prior is characterized by a low dimensional Gaussian distribution on initial momentum. This is achieved using principal component analysis (PCA) to construct the eigenspace of the initial momentum. A likelihood function is formulated as the conditional probability of observing surfaces given any particular value of the initial momentum, which is modeled as a random field of vector-valued measures characterizing the geometry of surfaces. We define the diffeomorphic mapping as a problem that maximizes a posterior distribution of the initial momentum given observable surfaces over the eigenspace of the initial momentum. We demonstrate the stability of the initial momentum eigenspace when altering training samples using a bootstrapping method. We then validate the mapping accuracy and show robustness to outliers whose shape variation is not incorporated into the shape prior.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6022802]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>302</startPage>
			<endPage>311</endPage>
			<fileSize>416</fileSize>
			<authors><![CDATA[Qiu, A.;Younes, L.;Miller, M. I.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Prior Shape Level Set Segmentation on Multistep Generated Probability Maps of MR Datasets for Fully Automatic Kidney Parenchyma Volumetry]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6022800]]></link>
			<description><![CDATA[Fully automatic 3-D segmentation techniques for clinical applications or epidemiological studies have proven to be a very challenging task in the domain of medical image analysis. 3-D organ segmentation on magnetic resonance (MR) datasets requires a well-designed segmentation strategy due to imaging artifacts, partial volume effects, and similar tissue properties of adjacent tissues. We developed a 3-D segmentation framework for fully automatic kidney parenchyma volumetry that uses Bayesian concepts for probability map generation. The probability map quality is improved in a multistep refinement approach. An extended prior shape level set segmentation method is then applied on the refined probability maps. The segmentation quality is improved by incorporating an exterior cortex edge alignment technique using cortex probability maps. In contrast to previous approaches, we combine several relevant kidney parenchyma features in a sequence of segmentation techniques for successful parenchyma delineation on native MR datasets. Furthermore, the proposed method is able to recognize and exclude parenchymal cysts from the parenchymal volume. We analyzed four different quality measures showing better results for right parenchymal tissue than for left parenchymal tissue due to an incorporated liver part removal in the segmentation framework. The results show that the outer cortex edge alignment approach successfully improves the quality measures.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6022800]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>312</startPage>
			<endPage>325</endPage>
			<fileSize>2339</fileSize>
			<authors><![CDATA[Gloger, O.;Tonnies, K. D.;Liebscher, V.;Kugelmann, B.;Laqua, R.;Volzke, H.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Incompressible Deformation Estimation Algorithm (IDEA) From Tagged MR Images]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6022801]]></link>
			<description><![CDATA[Measuring the 3D motion of muscular tissues, e.g., the heart or the tongue, using magnetic resonance (MR) tagging is typically carried out by interpolating the 2D motion information measured on orthogonal stacks of images. The incompressibility of muscle tissue is an important constraint on the reconstructed motion field and can significantly help to counter the sparsity and incompleteness of the available motion information. Previous methods utilizing this fact produced incompressible motions with limited accuracy. In this paper, we present an incompressible deformation estimation algorithm (IDEA) that reconstructs a dense representation of the 3D displacement field from tagged MR images and the estimated motion field is incompressible to high precision. At each imaged time frame, the tagged images are first processed to determine components of the displacement vector at each pixel relative to the reference time. IDEA then applies a smoothing, divergence-free, vector spline to interpolate velocity fields at intermediate discrete times such that the collection of velocity fields integrate over time to match the observed displacement components. Through this process, IDEA yields a dense estimate of a 3D displacement field that matches our observations and also corresponds to an incompressible motion. The method was validated with both numerical simulation and in vivo human experiments on the heart and the tongue.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6022801]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>326</startPage>
			<endPage>340</endPage>
			<fileSize>2974</fileSize>
			<authors><![CDATA[Liu, X.;Abd-Elmoniem, K. Z.;Stone, M.;Murano, E. Z.;Zhuo, J.;Gullapalli, R. P.;Prince, J. L.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Automatic Construction of Parts+Geometry Models for Initializing Groupwise Registration]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6025299]]></link>
			<description><![CDATA[Groupwise nonrigid image registration is a powerful tool to automatically establish correspondences across sets of images. Such correspondences are widely used for constructing statistical models of shape and appearance. As existing techniques usually treat registration as an optimization problem, a good initialization is required. Although the standard initialization&#x2014;affine transformation&#x2014;generally works well, it is often inadequate when registering images of complex structures. In this paper we present a more sophisticated method that uses the sparse matches of a parts+geometry model as the initialization. We show that both the model and its matches can be automatically obtained, and that the matches are able to effectively initialize a groupwise nonrigid registration algorithm, leading to accurate dense correspondences. We also show that the dense mesh models constructed during the groupwise registration process can be used to accurately annotate new images. We demonstrate the efficacy of the approach on three datasets of increasing difficulty, and report on a detailed quantitative evaluation of its performance.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6025299]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>341</startPage>
			<endPage>358</endPage>
			<fileSize>5529</fileSize>
			<authors><![CDATA[Zhang, P.;Cootes, T. F.;]]></authors>
		</item>
		<item>
			<title><![CDATA[A Semi-Markov Model for Mitosis Segmentation in Time-Lapse Phase Contrast Microscopy Image Sequences of Stem Cell Populations]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6026949]]></link>
			<description><![CDATA[We propose a semi-Markov model trained in a max-margin learning framework for mitosis event segmentation in large-scale time-lapse phase contrast microscopy image sequences of stem cell populations. Our method consists of three steps. First, we apply a constrained optimization based microscopy image segmentation method that exploits phase contrast optics to extract candidate subsequences in the input image sequence that contains mitosis events. Then, we apply a max-margin hidden conditional random field (MM-HCRF) classifier learned from human-annotated mitotic and nonmitotic sequences to classify each candidate subsequence as a mitosis or not. Finally, a max-margin semi-Markov model (MM-SMM) trained on manually-segmented mitotic sequences is utilized to reinforce the mitosis classification results, and to further segment each mitosis into four predefined temporal stages. The proposed method outperforms the event-detection CRF model recently reported by Huh <etal/> as well as several other competing methods in very challenging image sequences of multipolar-shaped C3H10T1/2 mesenchymal stem cells. For mitosis detection, an overall precision of 95.8% and a recall of 88.1% were achieved. For mitosis segmentation, the mean and standard deviation for the localization errors of the start and end points of all mitosis stages were well below 1 and 2 frames, respectively. In particular, an overall temporal location error of <formula formulatype="inline"><tex Notation="TeX">$0.73 pm 1.29$</tex></formula> frames was achieved for locating daughter cell birth events.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6026949]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>359</startPage>
			<endPage>369</endPage>
			<fileSize>1192</fileSize>
			<authors><![CDATA[Liu, A.-A.;Li, K.;Kanade, T.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Medusa: A Scalable MR Console Using USB]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6029455]]></link>
			<description><![CDATA[Magnetic resonance imaging (MRI) pulse sequence consoles typically employ closed proprietary hardware, software, and interfaces, making difficult any adaptation for innovative experimental technology. Yet MRI systems research is trending to higher channel count receivers, transmitters, gradient/shims, and unique interfaces for interventional applications. Customized console designs are now feasible for researchers with modern electronic components, but high data rates, synchronization, scalability, and cost present important challenges. Implementing large multichannel MR systems with efficiency and flexibility requires a scalable modular architecture. With Medusa, we propose an open system architecture using the universal serial bus (USB) for scalability, combined with distributed processing and buffering to address the high data rates and strict synchronization required by multichannel MRI. Medusa uses a modular design concept based on digital synthesizer, receiver, and gradient blocks, in conjunction with fast programmable logic for sampling and synchronization. Medusa is a form of synthetic instrument, being reconfigurable for a variety of medical/scientific instrumentation needs. The Medusa distributed architecture, scalability, and data bandwidth limits are presented, and its flexibility is demonstrated in a variety of novel MRI applications.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6029455]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>370</startPage>
			<endPage>379</endPage>
			<fileSize>1509</fileSize>
			<authors><![CDATA[Stang, P. P.;Conolly, S. M.;Santos, J. M.;Pauly, J. M.;Scott, G. C.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Evaluation of Segmentation Algorithms on Cell Populations Using CDF Curves]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6029989]]></link>
			<description><![CDATA[Cell segmentation is a critical step in the analysis pipeline for most imaging cytometry experiments and evaluating the performance of segmentation algorithms is important for aiding the selection of segmentation algorithms. Four popular algorithms are evaluated based on their cell segmentation performance. Because segmentation involves the classification of pixels belonging to regions within the cell or belonging to background, these algorithms are evaluated based on their total misclassification error. Misclassification error is particularly relevant in the analysis of quantitative descriptors of cell morphology involving pixel counts, such as projected area, aspect ratio and diameter. Since the cumulative distribution function captures completely the stochastic properties of a population of misclassification errors it is used to compare segmentation performance.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6029989]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>380</startPage>
			<endPage>390</endPage>
			<fileSize>1531</fileSize>
			<authors><![CDATA[Hagwood, C.;Bernal, J.;Halter, M.;Elliott, J.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Performance Analysis for Magnetic Resonance Imaging With Nonlinear Encoding Fields]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6030946]]></link>
			<description><![CDATA[Nonlinear spatial encoding fields for magnetic resonance imaging (MRI) hold great promise to improve on the linear gradient approaches by, for example, enabling reduced imaging times. Imaging schemes that employ general nonlinear encoding fields are difficult to analyze using traditional measures. In particular, the resolution is spatially varying, characterized by a position-dependent point spread function (PSF). Likewise, the use of nonlinear encoding fields creates an additional spatial dependence on the signal-to-noise ratio (SNR). Although the two properties of resolution and SNR are linked, in this work we focus on the latter. To this end, we examine the pixel variance, which requires a computation that is often not feasible for nonlinear encoding schemes. This paper presents a general formulation for the performance analysis of imaging schemes using arbitrary encoding fields. The analysis leads to the derivation of a practical and computationally efficient performance metric, which is demonstrated through simulation examples.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6030946]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>391</startPage>
			<endPage>404</endPage>
			<fileSize>1253</fileSize>
			<authors><![CDATA[Layton, K. J.;Morelande, M.;Farrell, P. M.;Moran, B.;Johnston, L. A.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Improved Regional Activity Quantitation in Nuclear Medicine Using a New Approach to Correct for Tissue Partial Volume and Spillover Effects]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6030947]]></link>
			<description><![CDATA[We have developed a new method of compensating for effects of partial volume and spillover in dual-modality imaging. The approach requires segmentation of just a few tissue types within a small volume-of-interest (VOI) surrounding a lesion; the algorithm estimates simultaneously, from projection data, the activity concentration within each segmented tissue inside the VOI. Measured emission projections were fitted to the sum of resolution-blurred projections of each such tissue, scaled by its unknown activity concentration, plus a global background contribution obtained by reprojection through the reconstructed image volume outside the VOI. The method was evaluated using multiple-pinhole <formula formulatype="inline"><tex Notation="TeX">$mu{rm SPECT}$</tex></formula> data simulated for the MOBY mouse phantom containing two spherical lung tumors and one liver tumor, as well as using multiple-bead phantom data acquired on <formula formulatype="inline"><tex Notation="TeX">$mu{rm SPECT}$</tex> </formula> and <formula formulatype="inline"><tex Notation="TeX">$mu{rm CT}$</tex></formula> scanners. Each VOI in the simulation study was 4.8 mm (12 voxels) cubed and, depending on location, contained up to four tissues (tumor, liver, heart, lung) with different values of relative <formula formulatype="inline"> <tex Notation="TeX">$^{99{rm m}}{rm Tc}$</tex></formula> concentration. All tumor activity estimates achieved <formula formulatype="inline"><tex Notation="TeX">${&lt;}{3%}$</tex> </formula> bias after <formula formulatype="inline"><tex Notation="TeX">${sim}{15}$</tex> </formula> ordered-subsets expectation maximization (OSEM) iterations <formula formulatype="inline"><tex Notation="TeX">$(times 10~{hbox {subsets}})$</tex> </formula>, with better than 8% precision (<formula formulatype="inline"> <tex Notation="TeX">${leq}{25%}$</tex></formula> greater than the Cramer&#x2013;Rao lower bound). The projection-based fitting approach also outperformed three stand-
rdized uptake value (SUV)-like metrics, one of which was corrected for count spillover. In the bead phantom experiment, the mean <formula formulatype="inline"> <tex Notation="TeX">${pm}$</tex></formula> standard deviation of the bias of VOI estimates of bead concentration were <formula formulatype="inline"> <tex Notation="TeX">$0.9pm 9.5%$</tex></formula>, comparable to those of a perturbation geometric transfer matrix (pGTM) approach <formula formulatype="inline"> <tex Notation="TeX">$({-}{5.4}pm 8.6%)$</tex></formula>; however, VOI estimates were more stable with increasing iteration number than pGTM estimates, even in the presence of substantial axial misalignment between <formula formulatype="inline"> <tex Notation="TeX">$mu{rm CT}$</tex></formula> and <formula formulatype="inline"> <tex Notation="TeX">$mu{rm SPECT}$</tex></formula> image volumes.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6030947]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>405</startPage>
			<endPage>416</endPage>
			<fileSize>1577</fileSize>
			<authors><![CDATA[Moore, S. C.;Southekal, S.;Park, M.-A.;McQuaid, S. J.;Kijewski, M. F.;Muller, S. P.;]]></authors>
		</item>
		<item>
			<title><![CDATA[High Range Resolution Ultrasonographic Vascular Imaging Using Frequency Domain Interferometry With the Capon Method]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6035979]]></link>
			<description><![CDATA[For high range resolution ultrasonographic vascular imaging, we apply frequency domain interferometry with the Capon method to a single frame of in-phase and quadrature (IQ) data acquired using a commercial ultrasonographic device with a 7.5 MHz linear array probe. In order to tailor the adaptive beamforming algorithm for ultrasonography we employ four techniques: frequency averaging, whitening, radio-frequency data oversampling, and the moving average. The proposed method had a range resolution of 0.05 mm in an ideal condition, and experimentally detected the boundary couple 0.17 mm apart, where the boundary couple was indistinguishable from a single boundary utilizing a B-mode image. Further, this algorithm could depict a swine femoral artery with a range beam width of 0.054 mm and an estimation error for the vessel wall thickness of 0.009 mm, whereas using a conventional method the range beam width and estimation error were 0.182 and 0.021 mm, respectively. The proposed method requires 7.7 s on a mobile PC with a single CPU for a <formula formulatype="inline"> <tex Notation="TeX">$1times 3~{hbox {cm}}$</tex></formula> region of interest. These findings indicate the potential of the proposed method for the improvement of range resolution in ultrasonography without deterioration in temporal resolution, resulting in enhanced detection of vessel stenosis.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6035979]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>417</startPage>
			<endPage>429</endPage>
			<fileSize>3053</fileSize>
			<authors><![CDATA[Taki, H.;Taki, K.;Sakamoto, T.;Yamakawa, M.;Shiina, T.;Kudo, M.;Sato, T.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Error Analysis of Nonconstant Admittivity for MR-Based Electric Property Imaging]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6036177]]></link>
			<description><![CDATA[Magnetic resonance electrical property tomography (MREPT) is a new imaging modality to visualize a distribution of admittivity <formula formulatype="inline"><tex Notation="TeX">$gamma=sigma+iomegavarepsilon$</tex> </formula> inside the human body where <formula formulatype="inline"><tex Notation="TeX">$sigma$</tex></formula> and <formula formulatype="inline"> <tex Notation="TeX">$varepsilon$</tex></formula> denote electrical conductivity and permittivity, respectively. Using B1 maps acquired by an magnetic resonance imaging scanner, it produces cross-sectional images of <formula formulatype="inline"> <tex Notation="TeX">$sigma$</tex></formula> and <formula formulatype="inline"> <tex Notation="TeX">$varepsilon$</tex></formula> at the Larmor frequency. Since current MREPT methods rely on an assumption of a locally homogeneous admittivity, there occurs a reconstruction error where this assumption fails. Rigorously analyzing the reconstruction error in MREPT, we showed that the error is fundamental and may cause technical difficulties in interpreting MREPT images of a general inhomogeneous object. We performed numerical simulations and phantom experiments to quantitatively support the error analysis. We compared the MREPT image reconstruction problem with that of magnetic resonance electrical impedance tomography (MREIT) to highlight distinct features of both methods to probe the same object in terms of its high- and low-frequency conductivity distributions, respectively. MREPT images showed large errors along boundaries where admittivity values changed whereas MREIT images showed no such boundary effects. Noting that MREIT makes use of the term neglected in MREPT, a novel MREPT admittivity image reconstruction method is proposed to deal with the boundary effects, which requires further investigation on the complex directional derivative in the real Euclidian space <formula formulatype="inline"><tex Notation="TeX">${BBR}^3$</tex></formula>.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6036177]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>430</startPage>
			<endPage>437</endPage>
			<fileSize>792</fileSize>
			<authors><![CDATA[Seo, J. K.;Kim, M.-O.;Lee, J.;Choi, N.;Woo, E. J.;Kim, H. J.;Kwon, O. I.;Kim, D.-H.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Super-Resolution in Respiratory Synchronized Positron Emission Tomography]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6042337]]></link>
			<description><![CDATA[Respiratory motion is a major source of reduced quality in positron emission tomography (PET). In order to minimize its effects, the use of respiratory synchronized acquisitions, leading to gated frames, has been suggested. Such frames, however, are of low signal-to-noise ratio (SNR) as they contain reduced statistics. Super-resolution (SR) techniques make use of the motion in a sequence of images in order to improve their quality. They aim at enhancing a low-resolution image belonging to a sequence of images representing different views of the same scene. In this work, a maximum a posteriori (MAP) super-resolution algorithm has been implemented and applied to respiratory gated PET images for motion compensation. An edge preserving Huber regularization term was used to ensure convergence. Motion fields were recovered using a B-spline based elastic registration algorithm. The performance of the SR algorithm was evaluated through the use of both simulated and clinical datasets by assessing image SNR, as well as the contrast, position and extent of the different lesions. Results were compared to summing the registered synchronized frames on both simulated and clinical datasets. The super-resolution image had higher SNR (by a factor of over 4 on average) and lesion contrast (by a factor of 2) than the single respiratory synchronized frame using the same reconstruction matrix size. In comparison to the motion corrected or the motion free images a similar SNR was obtained, while improvements of up to 20% in the recovered lesion size and contrast were measured. Finally, the recovered lesion locations on the SR images were systematically closer to the true simulated lesion positions. These observations concerning the SNR, lesion contrast and size were confirmed on two clinical datasets included in the study. In conclusion, the use of SR techniques applied to respiratory motion synchronized images lead to motion compensation combined with improved image SNR and contrast, wi-
hout any increase in the overall acquisition times.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6042337]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>438</startPage>
			<endPage>448</endPage>
			<fileSize>1174</fileSize>
			<authors><![CDATA[Wallach, D.;Lamare, F.;Kontaxakis, G.;Visvikis, D.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Automated 3-D Segmentation of Lungs With Lung Cancer in CT Data Using a Novel Robust Active Shape Model Approach]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6042336]]></link>
			<description><![CDATA[Segmentation of lungs with (large) lung cancer regions is a nontrivial problem. We present a new fully automated approach for segmentation of lungs with such high-density pathologies. Our method consists of two main processing steps. First, a novel robust active shape model (RASM) matching method is utilized to roughly segment the outline of the lungs. The initial position of the RASM is found by means of a rib cage detection method. Second, an optimal surface finding approach is utilized to further adapt the initial segmentation result to the lung. Left and right lungs are segmented individually. An evaluation on 30 data sets with 40 abnormal (lung cancer) and 20 normal left/right lungs resulted in an average Dice coefficient of <formula formulatype="inline"> <tex Notation="TeX">$0.975pm 0.006$</tex></formula> and a mean absolute surface distance error of <formula formulatype="inline"><tex Notation="TeX">$0.84pm 0.23~{hbox {mm}}$</tex></formula>, respectively. Experiments on the same 30 data sets showed that our methods delivered statistically significant better segmentation results, compared to two commercially available lung segmentation approaches. In addition, our RASM approach is generally applicable and suitable for large shape models.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6042336]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>449</startPage>
			<endPage>460</endPage>
			<fileSize>4362</fileSize>
			<authors><![CDATA[Sun, S.;Bauer, C.;Beichel, R.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Fully Automated Attenuation Measurement and Motion Correction in FLIP Image Sequences]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6043908]]></link>
			<description><![CDATA[Fluorescence loss in photobleaching (FLIP) is a method to study compartment connectivity in living cells. A FLIP sequence is obtained by alternatively bleaching a spot in a cell and acquiring an image of the complete cell. Connectivity is estimated by comparing fluorescence signal attenuation in different cell parts. The measurements of the fluorescence attenuation are hampered by the low signal to noise ratio of the FLIP sequences, by sudden sample shifts and by sample drift. This paper describes a method that estimates the attenuation by modeling photobleaching as exponentially decaying signals. Sudden motion artifacts are minimized by registering the frames of a FLIP sequence to target frames based on the estimated model and by removing frames that contain deformations. Linear motion (sample drift) is reduced by minimizing the entropy of the estimated attenuation coefficients. Experiments on 16 in vivo FLIP sequences of muscle cells in Drosophila show that the proposed method results in fluorescence attenuations similar to the manually identified gold standard, but with standard deviations of approximately 50 times smaller. As a result of this higher precision, cell compartment edges and details such as cell nuclei become clearly discernible. The main value of this method is that it uses a model of the bleaching process to correct motion and that the model based fluorescence intensity and attenuation estimates can be interpreted easily. The proposed method is fully automatic, and runs in approximately one minute per sequence, making it suitable for unsupervised batch processing of large data series.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6043908]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>461</startPage>
			<endPage>473</endPage>
			<fileSize>4384</fileSize>
			<authors><![CDATA[van de Giessen, M.;van der Laan, A.;Hendriks, E. A.;Vidorreta, M.;Reiber, J. H. C.;Jost, C. R.;Tanke, H. J.;Lelieveldt, B. P. F.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Supervoxel-Based Segmentation of Mitochondria in EM Image Stacks With Learned Shape Features]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6044718]]></link>
			<description><![CDATA[It is becoming increasingly clear that mitochondria play an important role in neural function. Recent studies show mitochondrial morphology to be crucial to cellular physiology and synaptic function and a link between mitochondrial defects and neuro-degenerative diseases is strongly suspected. Electron microscopy (EM), with its very high resolution in all three directions, is one of the key tools to look more closely into these issues but the huge amounts of data it produces make automated analysis necessary. State-of-the-art computer vision algorithms designed to operate on natural 2-D images tend to perform poorly when applied to EM data for a number of reasons. First, the sheer size of a typical EM volume renders most modern segmentation schemes intractable. Furthermore, most approaches ignore important shape cues, relying only on local statistics that easily become confused when confronted with noise and textures inherent in the data. Finally, the conventional assumption that strong image gradients always correspond to object boundaries is violated by the clutter of distracting membranes. In this work, we propose an automated graph partitioning scheme that addresses these issues. It reduces the computational complexity by operating on supervoxels instead of voxels, incorporates shape features capable of describing the 3-D shape of the target objects, and learns to recognize the distinctive appearance of true boundaries. Our experiments demonstrate that our approach is able to segment mitochondria at a performance level close to that of a human annotator, and outperforms a state-of-the-art 3-D segmentation technique.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6044718]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>474</startPage>
			<endPage>486</endPage>
			<fileSize>1859</fileSize>
			<authors><![CDATA[Lucchi, A.;Smith, K.;Achanta, R.;Knott, G.;Fua, P.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Cardiac Motion and Deformation Recovery From MRI: A Review]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6044719]]></link>
			<description><![CDATA[Magnetic resonance imaging (MRI) is a highly advanced and sophisticated imaging modality for cardiac motion tracking and analysis, capable of providing 3D analysis of global and regional cardiac function with great accuracy and reproducibility. In the past few years, numerous efforts have been devoted to cardiac motion recovery and deformation analysis from MR image sequences. Many approaches have been proposed for tracking cardiac motion and for computing deformation parameters and mechanical properties of the heart from a variety of cardiac MR imaging techniques. In this paper, an updated and critical review of cardiac motion tracking methods including major references and those proposed in the past ten years is provided. The MR imaging and analysis techniques surveyed are based on cine MRI, tagged MRI, phase contrast MRI, DENSE, and SENC. This paper can serve as a tutorial for new researchers entering the field.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6044719]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>487</startPage>
			<endPage>503</endPage>
			<fileSize>347</fileSize>
			<authors><![CDATA[Wang, H.;Amini, A. A.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Robustness of Quantitative Compressive Sensing MRI: The Effect of Random Undersampling Patterns on Derived Parameters for DCE- and DSC-MRI]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6046135]]></link>
			<description><![CDATA[Compressive sensing (CS) in Cartesian magnetic resonance imaging (MRI) involves random partial Fourier acquisitions. The random nature of these acquisitions can lead to variance in reconstruction errors. In quantitative MRI, variance in the reconstructed images translates to an uncertainty in the derived quantitative maps. We show that for a spatially regularized 2<formula formulatype="inline"> <tex Notation="TeX">$times$</tex></formula>-accelerated human breast CS DCE-MRI acquisition with a 192<formula formulatype="inline"><tex Notation="TeX">$^{2}$</tex> </formula> matrix size, the coefficients of variation (CoVs) in voxel-level parameters due to the random acquisition are 1.1%, 0.96%, and 1.5% for the tissue parameters <formula formulatype="inline"><tex Notation="TeX">$K^{rm trans}$</tex></formula>, <formula formulatype="inline"><tex Notation="TeX">$v_{rm e}$</tex></formula>, and <formula formulatype="inline"><tex Notation="TeX">$v_{rm p}$</tex></formula>, with an average error in the mean of <formula formulatype="inline"> <tex Notation="TeX">$-$</tex></formula>2.5%, <formula formulatype="inline"> <tex Notation="TeX">$-$</tex></formula>2.0%, and <formula formulatype="inline"> <tex Notation="TeX">$-$</tex></formula>3.7%, respectively. Only 5% of the acquisition schemes had a systematic underestimation larger than than 4.2%, 3.7%, and 6.1%, respectively. For a 2<formula formulatype="inline"><tex Notation="TeX">$times$</tex> </formula>-accelerated rat brain CS DSC-MRI study with a <formula formulatype="inline"> <tex Notation="TeX">$64^{2}$</tex></formula> matrix size, the CoVs due to the random acquisition were 19%, 9.5%, and 15% for the cerebral blood flow and blood volume and mean transit time, respectively, and the average errors in the tumor mean were 9.2%, 0.49%, and <formula formulatype="inline"><tex Notation="TeX">$-$</tex></formula>7.0%, respectively. Across 11<formula formulatype="inline"> <tex Notation="TeX">$thinspace$</tex></formula>000 different -
S reconstructions, we saw no outliers in the distribution of parameters, suggesting that, despite the random undersampling schemes, CS accelerated quantitative MRI may have a predictable level of performance.]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6046135]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>504</startPage>
			<endPage>511</endPage>
			<fileSize>751</fileSize>
			<authors><![CDATA[Smith, D. S.;Li, X.;Gambrell, J. V.;Arlinghaus, L. R.;Quarles, C. C.;Yankeelov, T. E.;Welch, E. B.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Robust Statistical Fusion of Image Labels]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6046134]]></link>
			<description><![CDATA[Image labeling and parcellation (i.e., assigning structure to a collection of voxels) are critical tasks for the assessment of volumetric and morphometric features in medical imaging data. The process of image labeling is inherently error prone as images are corrupted by noise and artifacts. Even expert interpretations are subject to subjectivity and the precision of the individual raters. Hence, all labels must be considered imperfect with some degree of inherent variability. One may seek multiple independent assessments to both reduce this variability and quantify the degree of uncertainty. Existing techniques have exploited maximum a posteriori statistics to combine data from multiple raters and simultaneously estimate rater reliabilities. Although quite successful, wide-scale application has been hampered by unstable estimation with practical datasets, for example, with label sets with small or thin objects to be labeled or with partial or limited datasets. As well, these approaches have required each rater to generate a complete dataset, which is often impossible given both human foibles and the typical turnover rate of raters in a research or clinical environment. Herein, we propose a robust approach to improve estimation performance with small anatomical structures, allow for missing data, account for repeated label sets, and utilize training/catch trial data. With this approach, numerous raters can label small, overlapping portions of a large dataset, and rater heterogeneity can be robustly controlled while simultaneously estimating a single, reliable label set and characterizing uncertainty. The proposed approach enables many individuals to collaborate in the construction of large datasets for labeling tasks (e.g., human parallel processing) and reduces the otherwise detrimental impact of rater unavailability]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6046134]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>512</startPage>
			<endPage>522</endPage>
			<fileSize>833</fileSize>
			<authors><![CDATA[Landman, B. A.;Asman, A. J.;Scoggins, A. G.;Bogovic, J. A.;Xing, F.;Prince, J. L.;]]></authors>
		</item>
		<item>
			<title><![CDATA[Explore IEL IEEE's most comprehensive resource]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6142693]]></link>
			<description><![CDATA[ ]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6142693]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>523</startPage>
			<endPage>523</endPage>
			<fileSize>345</fileSize>
			<authors><![CDATA[]]></authors>
		</item>
		<item>
			<title><![CDATA[Have you visited lately? www.ieee.org]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6142694]]></link>
			<description><![CDATA[ ]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6142694]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>524</startPage>
			<endPage>524</endPage>
			<fileSize>210</fileSize>
			<authors><![CDATA[]]></authors>
		</item>
		<item>
			<title><![CDATA[IEEE Transactions on Medical Imaging information for authors]]></title>
			<link><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6142692]]></link>
			<description><![CDATA[ ]]></description>
			<pubDate><![CDATA[Feb.  2012]]></pubDate>
			<guid><![CDATA[http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=6142636&arnumber=6142692]]></guid>
			<volume>31</volume>
			<issue>2</issue>
			<startPage>C3</startPage>
			<endPage>C3</endPage>
			<fileSize>26</fileSize>
			<authors><![CDATA[]]></authors>
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