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Effects of physiological noise in population analysis of diffusion tensor MRI data

NEUROimage 2011年第2期54卷 1168-1177页

作者： Walker, Lindsay Chang, Lin-Ching Koay, Cheng Guan Sharma, Nik Cohen, Leonardo Verma, Ragini Pierpaoli, Carlo Eunice Kennedy Shriver Natl Inst Child Hlth & Hum Sect Tissue Biophys & Biomimet Program Pediat Imaging & Tissue Sci NIH Bethesda MD USA Catholic Univ Amer Dept Elect Engn & Comp Sci Washington DC 20064 USA Natl Inst Neurol Disorders & Stroke NIH Bethesda MD USA Univ Penn Dept Radiol Philadelphia PA 19104 USA

The goal of this study is to characterize the potential effect of artifacts originating from physiological noise on statistical analysis of diffusion tensor MRI (DTI) data in a population. DTI derived quantities including mean diffusivity (Trace(D)), fractional anisotropy (FA), and principal eigenvector (epsilon(1)) are computed in the brain of 40 healthy subjects from tensors estimated using two different methods: conventional nonlinear least-squares, and robust fitting (RESTORE). RESTORE identifies artifactual data points as outliers and excludes them on a voxel-by-voxel basis. We found that outlier data points are localized in specific spatial clusters in the population, indicating a consistency in brain regions affected across subjects. In brain parenchyma RESTORE slightly reduces inter-subject variance of FA and Trace(D). The dominant effect of artifacts, however, is bias. Voxel-wise analysis indicates that inclusion of outlier data points results in clusters of under- and over-estimation of FA, while Trace(D) is always over-estimated. Removing outliers affects epsilon(1) mostly in low anisotropy regions. It was found that brain regions known to be affected by cardiac pulsation - cerebellum and genu of the corpus callosum, as well as regions not previously reported, splenium of the corpus callosum-show significant effects in the population analysis. It is generally assumed that statistical properties of DTI data are homogenous across the brain. This assumption does not appear to be valid based on these results. The use of RESTORE can lead to a more accurate evaluation of a population, and help reduce spurious findings that may occur due to artifacts in DTI data. Published by Elsevier Inc.

关键词： Adult Anisotropy Artifacts Brain Mapping/methods Brain Mapping/methods Diffusion Magnetic Resonance Imaging Female Humans image processing, computer-assisted/methods

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A hybrid approach to automatic clustering of white matter fibers

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NEUROimage 2010年第2期49卷 1249-1258页

作者： Li, Hai Xue, Zhong Guo, Lei Liu, Tianming Hunter, Jill Wong, Stephen T. C. Cornell Univ Med Image Anal Lab Ctr Bioengn & Informat Methodist HospRes Inst Houston TX USA Cornell Univ Dept Radiol Methodist Hosp Weill Med Coll Houston TX USA Univ Georgia Dept Comp Sci Athens GA 30602 USA Univ Georgia Bioimaging Res Ctr Athens GA 30602 USA Texas Childrens Hosp Neuroradiol Sect Dept Radiol Houston TX 77030 USA

Recently, the tract-based white matter (WM) fiber analysis has been recognized as an effective framework to study the diffusion tensor imaging (DTI) data of human brain. This framework can provide biologically meaningful results and facilitate the tract-based comparison across subjects. However, due to the lack of quantitative definition of WM bundle boundaries, the complexity of brain architecture and the variability of WM shapes, clustering WM fibers into anatomically meaningful bundles is nontrivial. In this paper, we propose a hybrid top-down and bottom-up approach for automatic clustering and labeling of WM fibers, which utilizes both brain parcellation results and similarities between WM fibers. Our experimental results show reasonably good performance of this approach in clustering WM fibers into anatomically meaningful bundles. (C) 2009 Elsevier Inc. All rights reserved.

关键词： Algorithms Automation Brain/anatomy & histology Cluster Analysis Databases as Topic Diffusion Tensor Imaging/methods Diffusion Tensor Imaging/methods Fuzzy Logic Humans image processing, computer-assisted/methods Nerve Fibers, Myelinated Neural Pathways/anatomy & histology Organ Size

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Specific, Sensitive, High-Resolution Detection of Protein Molecules in Eukaryotic Cells Using Metal-Tagging Transmission Electron Microscopy

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STRUCTURE 2012年第5期20卷 759-766页

作者： Risco, Cristina Sanmartin-Conesa, Eva Tzeng, Wen-Pin Frey, Teryl K. Seybold, Volker de Groot, Raoul J. Ctr Nacl Biotecnol CSIC Cell Struct Lab Madrid 28049 Spain Georgia State Univ Dept Biol Atlanta GA 30302 USA Carl Zeiss Nano Technol Syst GmbH Applicat Dev Transmiss Electron Microscopy D-73447 Oberkochen Germany Univ Utrecht Fac Vet Med Div Virol Dept Infect Dis & Immunol NL-3584 CL Utrecht Netherlands

More than any other methodology, transmission electron microscopy (TEM) has contributed to our understanding of the architecture and organization of cells. With current detection limits approaching atomic resolution, it will ultimately become possible to ultrastructurally image intracellular macromolecular assemblies in situ. Presently, however, methods to unambiguously identify proteins within the crowded environment of the cell's interior are lagging behind. We describe an approach, metal-tagging TEM (METTEM), that allows detection of intracellular proteins in mammalian cells with high specificity, exceptional sensitivity, and at molecular scale resolution. In live cells treated with gold salts, proteins bearing a small metal-binding tag will form 1-nm gold nanoclusters, readily detectable in electron micrographs. The applicability and strength of METTEM is demonstrated by a study of Rubella virus replicase and capsid proteins, which revealed virus-induced cell structures not seen before.

关键词： Capsid Proteins/chemistry Capsid Proteins/metabolism Cells, Cultured Cellular Structures/ultrastructure Eukaryotic Cells/metabolism Gold/chemistry image processing, computer-assisted/methods Metallothionein/chemistry Metallothionein/metabolism Metallothionein/ultrastructure Metals/chemistry Metals/metabolism Microscopy, Electron, Transmission/methods Microscopy, Fluorescence Protein Conformation Proteins/chemistry Proteins/ultrastructure Rubella virus/enzymology Rubella virus/metabolism Sensitivity and Specificity Viral Proteins/chemistry

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Comparing surface-based and volume-based analyses of functional neuroimaging data in patients with schizophrenia

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NEUROimage 2008年第3期41卷 835-848页

作者： Anticevic, Alan Dierker, Donna L. Gillespie, Sarah K. Repovs, Grega Csernansky, John G. Van Essen, David C. Barch, Deanna M. Washington Univ Dept Psychol St Louis MO 63130 USA Washington Univ Sch Med Dept Anat & Neurobiol St Louis MO 63110 USA Washington Univ Sch Med Dept Psychiat St Louis MO 63110 USA

A major challenge in functional neuroimaging is to cope with individual variability in cortical structure and function. Most analyses of cortical function compensate for variability using affine or low-dimensional nonlinear volume-based registration (VBR) of individual subjects to an atlas, which does not explicitly take into account the geometry of cortical convolutions. A promising alternative is to use surface-based registration (SBR), which capitalizes on explicit surface representations of cortical folding patterns in individual subjects. In this study, we directly compare results from SBR and affine VBR in a study of working memory in healthy controls and patients with schizophrenia (SCZ). Each subject's structural scan was used for cortical surface reconstruction using the SureFit method. fMRI data were mapped directly onto individual cortical surface models, and each hemisphere was registered to the population-average PALS-B12 atlas using landmark-constrained SBR. The precision with which cortical sulci were aligned was much greater for SBR than VBR. SBR produced superior alignment precision across the entire cortex, and this benefit was greater in patients with schizophrenia. We demonstrate that spatial smoothing on the surface provides better resolution and signal preservation than a comparable degree of smoothing in the volume domain. Lastly, the statistical power of functional activation in the working memory task was greater for SBR than for VBR. These results indicate that SBR provides significant advantages over affine VBR when analyzing cortical fMRI activations. Furthermore, these improvements can be even greater in disorders that have associated structural abnormalities. (C) 2008 Elsevier Inc. All rights reserved.

关键词： Adult Brain/anatomy & histology Brain/physiology Brain Mapping/methods Brain Mapping/methods Female Humans image processing, computer-assisted/methods Magnetic Resonance Imaging Male Memory/physiology Schizophrenia/pathology Schizophrenia/physiopathology

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The future of acquisition speed, coverage, sensitivity, and resolution

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NEUROimage 2012年第2期62卷 1221-1229页

作者： Wald, Lawrence L. Harvard Univ Sch Med Boston MA USA MIT Harvard MIT Div Hlth Sci & Technol Charlestown MA USA Massachusetts Gen Hosp AA Martinos Ctr Biomed Imaging Dept Radiol Boston MA 02129 USA

Two decades of technology development has continually improved the image quality, spatial-temporal resolution, and sensitivity of the fMRI acquisition. In this article, I assess our current acquisition needs, briefly examine the technological breakthroughs that have benefited fMRI in the past, and look at some promising technologies that are currently under development to try to envision what the fMRI acquisition protocol of the future might look like. (C) 2012 Elsevier Inc. All rights reserved.

关键词： Brain Mapping/history Brain Mapping/history Brain Mapping/methods Brain Mapping/methods Brain Mapping/trends Brain Mapping/trends History, 20th Century History, 21st Century image processing, computer-assisted/history image processing, computer-assisted/methods image processing, computer-assisted/trends Magnetic Resonance Imaging/history Magnetic Resonance Imaging/methods Magnetic Resonance Imaging/trends

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Ultra high-resolution fMRI in monkeys with implanted RF coils

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NEURON 2002年第2期35卷 227-242页

作者： Logothetis, NK Merkle, H Augath, M Trinath, T Ugurbil, K Max Planck Inst Biol Cybernet D-72076 Tubingen Germany Univ Minnesota Dept Radiol Ctr Magnet Resonance Res Minneapolis MN 55455 USA

Spatiotemporally resolved functional MRI (fMRI) in animals can reveal how wide-spread neural networks are organized and accompanying electrophysiological recordings can show how small neural assemblies contribute to this organization. Here we present a novel technique that yields high-resolution structural and functional images of the monkey brain with small, tissue-compatible, intraosteally implantable radiofrequency coils. Voxel sizes as small as 0.0113 mul with high signal-to-noise and contrast-to-noise ratios were obtained, revealing both structural and functional cortical architecture in great detail. Up to a certain point, contrast sensitivity increased with decreasing voxel size, probably because of the decreased partial volume effects. Spatial specificity was demonstrated by the lamina-specific activation in experiments comparing responses to moving and flickering stimuli. The implications of this technique for combined fMRI/electrophysiology experiments and its limitations in terms of spatial coverage are discussed.

关键词： Animals Brain Mapping/instrumentation Brain Mapping/instrumentation Brain Mapping/methods Brain Mapping/methods Cerebral Cortex/anatomy & histology Cerebral Cortex/physiology Cerebrovascular Circulation/physiology Electrodes, Implanted/standards Electrodes, Implanted/standards Electrodes, Implanted/trends Electrodes, Implanted/trends Evoked Potentials, Visual/physiology Haplorhini/anatomy & histology Haplorhini/physiology Haplorhini/surgery image processing, computer-assisted/instrumentation image processing, computer-assisted/methods Magnetic Resonance Imaging/instrumentation Magnetic Resonance Imaging/methods Nerve Net/anatomy & histology Nerve Net/physiology Neurophysiology/instrumentation Neurophysiology/methods Neurosurgical Procedures/instrumentation Neurosurgical Procedures/methods Photic Stimulation Radio Waves/diagnostic use Radio Waves/diagnostic use Skull/anatomy & histology Skull/surgery Visual Cortex/anatomy & histology Visual Cortex/physiology

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SPM analysis of parametric (R)-[¹¹C]PK11195 binding images:: Plasma input versus reference tissue parametric methods

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NEUROimage 2007年第4期35卷 1473-1479页

作者： Schuitemaker, Alie van Berckel, Bart N. M. Kropholler, Marc A. Veltman, Dick J. Scheltens, Philip Jonker, Cees Lammertsma, AdrIaan A. Boellaard, Ronald VU Univ Med Ctr Dept Nucl Med & PET Res NL-1081 MB Amsterdam Netherlands VU Univ Med Ctr Dept Neurol Alzheimer Ctr NL-1081 HV Amsterdam Netherlands VU Univ Med Ctr Dept Psychiat NL-1081 HV Amsterdam Netherlands

(R)-[C-11]PK11195 has been used for quantifying cerebral microglial activation in vivo. In previous studies, both plasma input and reference tissue methods have been used, usually in combination with a region of interest (ROI) approach. Definition of ROIs, however, can be labourious and prone to interobserver variation. In addition, results are only obtained for predefined areas and (unexpected) signals in undefined areas may be missed. On the other hand, standard pharmacokinetic models are too sensitive to noise to calculate (R)[C-11]PK11195 binding on a voxel-by-voxel basis. Linearised versions of both plasma input and reference tissue models have been described, and these are more suitable for parametric imaging. The purpose of this study was to compare the performance of these plasma input and reference tissue parametric methods on the outcome of statistical parametric mapping (SPM) analysis of (R)-[C-11]PK11195 binding. Dynamic (R)-[C-11]-PK11195 PET scans with arterial blood sampling were performed in 7 younger and 11 elderly healthy subjects. Parametric images of volume of distribution (V-d) and binding potential (BP) were generated using linearised versions of plasma input (Logan) and reference tissue (Reference Parametric Mapping) models. images were compared at the group level using SPM with a two-sample t-test per voxel, both with and without proportional scaling. Parametric BP images without scaling provided the most sensitive framework for determining differences in (R)[C-11]PK11195 binding between younger and elderly subjects. V-d images could only demonstrate differences in (R)-[C-11]PK11195 binding when analysed with proportional scaling due to intersubject variation in K-1/k(2) (blood-brain barrier transport and non-specific binding). (c) 2007 Elsevier Inc. All rights reserved.

关键词： Adult Aged Aging/metabolism Brain/metabolism Brain/radionuclide imaging Data Interpretation, Statistical Female Functional Laterality/physiology Humans image processing, computer-assisted/methods Isoquinolines/blood Isoquinolines/metabolism Male Middle Aged Positron-Emission Tomography Radiopharmaceuticals/blood Radiopharmaceuticals/blood Radiopharmaceuticals/metabolism Radiopharmaceuticals/metabolism Tissue Distribution

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computer vision-based automated peak picking applied to protein NMR spectra

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BIOINFORMATICS 2015年第18期31卷 2981-2988页

作者： Klukowski, Piotr Walczak, Michal J. Gonczarek, Adam Boudet, Julien Wider, Gerhard Wroclaw Univ Technol Dept Comp Sci PL-50370 Wroclaw Poland ETH Inst Mol Biol & Biophys CH-8093 Zurich Switzerland

Motivation: A detailed analysis of multidimensional NMR spectra of macromolecules requires the identification of individual resonances (peaks). This task can be tedious and time-consuming and often requires support by experienced users. Automated peak picking algorithms were introduced more than 25 years ago, but there are still major deficiencies/flaws that often prevent complete and error free peak picking of biological macromolecule spectra. The major challenges of automated peak picking algorithms is both the distinction of artifacts from real peaks particularly from those with irregular shapes and also picking peaks in spectral regions with overlapping resonances which are very hard to resolve by existing computer algorithms. In both of these cases a visual inspection approach could be more effective than a 'blind' algorithm. Results: We present a novel approach using computer vision (CV) methodology which could be better adapted to the problem of peak recognition. After suitable 'training' we successfully applied the CV algorithm to spectra of medium-sized soluble proteins up to molecular weights of 26 kDa and to a 130 kDa complex of a tetrameric membrane protein in detergent micelles. Our CV approach outperforms commonly used programs. With suitable training datasets the application of the presented method can be extended to automated peak picking in multidimensional spectra of nucleic acids or carbohydrates and adapted to solid-state NMR spectra.

关键词： Algorithms Humans image processing, computer-assisted/methods Nuclear Magnetic Resonance, Biomolecular/methods Pattern Recognition, Visual Proteins/chemistry

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Measurement and reduction of motion and ballistocardiogram artefacts from simultaneous EEG and fMRI recordings

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NEUROimage 2007年第1期37卷 202-211页

作者： Masterton, Richard A. J. Abbott, David F. Fleming, Steven W. Jackson, Graeme D. Brain Res Inst Heidelberg Vic 3081 Australia Univ Melbourne Dept Med Parkville Vic 3010 Australia Univ Melbourne Dept Radiol Parkville Vic 3010 Australia

Recording the electroencephalogram (EEG) during functional magnetic resonance imaging (fMRI) permits the identification of haemodynamic changes associated with EEG events. However, subject motion within the MR scanner can cause unpredictable and frustrating artefacts on the EEG that may appear focally, bilaterally or unilaterally and can sometimes be confused for epileptiform activity. Motion may arise from a number of sources: small involuntary cardiac-related body movements (ballistocardiogram);acoustic vibrations due to the scanner machinery;and voluntary subject movements. Here we describe a new real-time technique for removing ballistocardiogram (BCG) and movement artefact from EEG recordings in the MR scanner using a novel method for recording subject motion. We record the current induced in a number of wire loops, attached to a cap worn by the subject, due to motion in the static magnetic field of the scanner (Faraday's Law). This is the same process that leads to the motion artefacts on the EEG, and hence these signals are ideally suited to filtering these artefacts from the EEG. Our filter uses a linear adaptive technique based upon the Recursive Least Squares (RLS) algorithm. We demonstrate in both simulations and real EEG recordings from epilepsy patients that our filter significantly reduces the artefact power whilst preserving the underlying EEG signal. (c) 2007 Elsevier Inc. All rights reserved.

关键词： Action Potentials/physiology Adult Artifacts Ballistocardiography Cerebral Cortex/physiopathology computer Simulation Electroencephalography/methods Epilepsy/diagnosis Epilepsy/physiopathology Female Fourier Analysis Fourier Analysis Humans image processing, computer-assisted/methods Least-Squares Analysis Magnetic Resonance Imaging/methods Male Middle Aged Reference Values Reproducibility of Results Signal processing, computer-assisted Software

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Real-time support vector classification and feedback of multiple emotional brain states

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NEUROimage 2011年第2期56卷 753-765页

作者： Sitaram, Ranganatha Lee, Sangkyun Ruiz, Sergio Rana, Mohit Veit, Ralf Birbaumer, Niels Univ Tubingen Inst Med Psychol & Behav Neurobiol D-72074 Tubingen Germany Int Max Planck Res Sch Grad Sch Neural & Behav Sci D-72074 Tubingen Germany Osped San Camillo Ist Ricovero & Curs Carattere Sci Venice Lido Italy Pontificia Univ Catolica Chile Dept Psychiat Fac Med Santiago Chile

An important question that confronts current research in affective neuroscience as well as in the treatment of emotional disorders is whether it is possible to determine the emotional state of a person based on the measurement of brain activity alone. Here, we first show that an online support vector machine (SVM) can be built to recognize two discrete emotional states, such as happiness and disgust from fMRI signals, in healthy individuals instructed to recall emotionally salient episodes from their lives. We report the first application of real-time head motion correction, spatial smoothing and feature selection based on a new method called Effect mapping. The classifier also showed robust prediction rates in decoding three discrete emotional states (happiness, disgust and sadness) in an extended group of participants. Subjective reports ascertained that participants performed emotion imagery and that the online classifier decoded emotions and not arbitrary states of the brain. Offline whole brain classification as well as region-of-interest classification in 24 brain areas previously implicated in emotion processing revealed that the frontal cortex was critically involved in emotion induction by imagery. We also demonstrate an fMRI-BCI based on real-time classification of BOLD signals from multiple brain regions, for each repetition time (TR) of scanning, providing visual feedback of emotional states to the participant for potential applications in the clinical treatment of dysfunctional affect. (C) 2010 Elsevier Inc. All rights reserved.

关键词： Adult Artificial Intelligence Brain/physiology Brain Mapping/methods Brain Mapping/methods Emotions/physiology Humans image processing, computer-assisted/methods Magnetic Resonance Imaging Young Adult

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