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Using SPM normalization for lesion analysis in spatial neglect

BRAIN 2004年第4期127卷 E10-U3页

作者： Karnath, HO Fruhmann Berger, M Zopf, R Küker, W Univ Tubingen Hertie Inst Clin Brain Res Dept Cognit Neurol D-72076 Tubingen Germany Univ Tubingen Dept Neuroradiol D-72076 Tubingen Germany

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Lattice parameters from direct-space images at two tilts

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ULTRAMICROSCOPY 2003年第3-4期94卷 245-262页

作者： Qin, W Fraundorf, P Univ Missouri Ctr Mol Elect St Louis MO 63121 USA

Lattices in three dimensions are oft studied from the "reciprocal space" perspective of diffraction. Today, the full lattice of a crystal can often be inferred from direct-space information about three sets of non-parallel lattice planes. Such data can come from electron-phase (or less easily Z contrast images) taken at two tilts, provided that one image shows two non-parallel lattice periodicities, and the other shows a periodicity not coplanar with the first two. We outline here protocols for measuring the 3D parameters of cubic lattice types in this way. For randomly oriented nanocrystals with cell side greater than twice the continuous transfer limit, orthogonal +/- 15degrees and +/- 10degrees tilt ranges might allow one to measure 3D parameters of all such lattice types in a specimen from only two well-chosen images. The strategy is illustrated by measuring the lattice parameters of a 10 nm WC1-x crystal in a plasma-enhanced chemical-vapor deposited thin film. (C) 2002 Elsevier Science B.V. All rights reserved.

关键词： Algorithms Crystallization/methods image processing, computer-assisted/methods Microscopy, Electron/methods Research Design/statistics & numerical data

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Automatic segmentation of thalamic nuclei from diffusion tensor magnetic resonance imaging

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NEUROimage 2003年第2期19卷 391-401页

作者： Wiegell, MR Tuch, DS Larsson, HBW Wedeen, VJ Massachusetts Gen Hosp Athinoula A Martinos Ctr Biomed Imaging Charlestown MA 02129 USA Hvidovre Univ Hosp Danish Res Ctr Magnet Resonance DK-2650 Hvidovre Denmark Harvard Univ MIT Div Hlth Sci & Technol Cambridge MA 02139 USA

The nuclei of the thalamus have traditionally been delineated by their distinct cyto/myeloarchitectural appearance on histology. Here, we show that diffusion tensor magnetic resonance imaging (DTI) can noninvasively resolve the major thalamic nuclei based on the characteristic fiber orientation of the corticothalamic/thalamocortical striations within each nucleus. Using an automatic clustering algorithm, we extracted the Talairach coordinates for the individual thalamic nuclei. The center-of-mass coordinates for the segmented nuclei were found to agree strongly with those obtained from a histological atlas. The ability to resolve thalamic nuclei with DTI will allow for morphometric analysis of specific nuclei and improved anatomical localization of functional activation in the thalamus. (C) 2003 Elsevier Science (USA). All rights reserved.

关键词： Algorithms Brain Mapping/methods Brain Mapping/methods Cerebral Cortex/anatomy & histology Diffusion Magnetic Resonance Imaging/methods Dominance, Cerebral/physiology Humans image processing, computer-assisted/methods Neural Pathways/anatomy & histology Sensitivity and Specificity Synaptic Transmission/physiology Thalamic Nuclei/anatomy & histology

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Testing effects of signal transduction pathways on cadherin junctional complex assembly using quantitative image analysis

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methods 2003年第3期30卷 218-227页

作者： Gopalakrishnan, S Dunn, KW Marrs, JA Indiana Univ Sch Med Dept Med Indianapolis IN 46202 USA

Cadherin adhesion molecules function in numerous cell biological processes that influence embryo development, normal cell physiology, and pathophysiology of many disease processes. Cadherins nucleate the assembly of the adherens junction, a cell-to-cell adhesion plaque that is prominent in simple epithelial cells and found in many cell types. Numerous cell biological approaches have been used to study this interesting class of molecules. Here, we outline methodology used in our studies of junctional complexes to examine effects of signaling molecules on assembly mechanisms. This is a quantitative method that allows the investigator to test the combined effect of two different signaling processes to determine whether these two signals act in concert within the same pathway. We discuss how this method could be generalized to other studies to examine consequences of various experimental manipulations on the assembly of cellular structures. (C) 2003 Elsevier Science (USA). All rights reserved.

关键词： Cadherins/physiology Epithelial Cells/physiology image processing, computer-assisted/methods Intercellular Junctions/physiology Signal Transduction/physiology Software

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Newly developed 3D endoscopic system: Preliminary experience

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ENDOSCOPY 2003年第2期35卷 181-184页

作者： Yoshida, T Inoue, H Hara, E Ohtsuka, K Endo, S Tamegai, Y Kashida, H Tanaka, J Kudo, S Showa Univ No Yokohama Hosp Ctr Digest Dis Tsuzuki Ku Yokohama Kanagawa 2248503 Japan

Although there have been earlier reports on the use of three-dimensional endoscopic systems in the gastrointestinal tract, real-time three-dimensional imaging has not previously been described. This paper presents experience in three cases with a novel endoscopic system for three-dimensional observation in clinical situations. Case 1 was a hyperplastic gastric polyp, the shape of which was considerably enhanced in comparison with two-dimensional endoscopic viewing. Case 2 was an advanced esophageal cancer, in which the sense of depth was improved in the esophagus. Case 3 was a depressed early gastric cancer, the shape of which was also enhanced. Between July 2001 and March 2002, three experienced endoscopists also used this new system in a further 34 patients, A three-dimensional endoscopic environment was visible with the system in all patients, and all of the endoscopists were able to obtain visual information regarding spatial depth. This experience suggests that the three-dimensional video-endoscopic system used here can be of value in gastrointestinal endoscopy.

关键词： Endoscopy, Gastrointestinal/methods Esophageal Neoplasms/diagnosis Humans image processing, computer-assisted/methods Imaging, Three-Dimensional Polyps/diagnosis Stomach Neoplasms/diagnosis Video Recording

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Optimized EPI for fMRI studies of the orbitofrontal cortex

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NEUROimage 2003年第2期19卷 430-441页

作者： Deichmann, R Gottfried, JA Hutton, C Turner, R Inst Neurol Wellcome Dept Imaging Neurosci London WC1N 3BG England

A common problem in gradient-echo echo planar imaging (EPI) is the occurrence of image distortions and signal losses caused by susceptibility gradients near air/tissue interfaces. Since EPI is frequently used for functional magnetic resonance imaging experiments based on the blood oxygenation level-dependent effect, functional studies of certain brain regions affected by susceptibility gradients, such as the temporal lobes and the orbitofrontal cortex, may be compromised. In this work a method for signal recovery in certain regions of the orbitofrontal cortex is presented. The influence of in-plane susceptibility gradients is reduced by optimization of the imaging slice orientation. Through-plane susceptibility gradients are partly compensated by means of a moderate preparation gradient pulse similar to z-shimming. In contrast to several other techniques proposed in the literature for reducing susceptibility effects, this method does not compromise the temporal resolution and is therefore applicable to event-related studies. (C) 2003 Elsevier Science (USA). All rights reserved.

关键词： Algorithms Artifacts Brain Mapping/methods Brain Mapping/methods Echo-Planar Imaging/methods Evoked Potentials/physiology Frontal Lobe/physiology Humans image Enhancement/methods image processing, computer-assisted/methods Magnetic Resonance Imaging/methods Mathematical Computing Oxygen Consumption/physiology Reference Values Sensitivity and Specificity

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SignalViewer: analyzing microarray images

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BIOINFORMATICS 2003年第13期19卷 1716-1717页

作者： Laws, RJ Bergemann, TL Quiaoit, F Zhao, LP Fred Hutchinson Canc Res Ctr Quantitat Genet Epidemiol Seattle WA 98109 USA

Microarray technology is now routinely used to monitor genome-wide expression profiles. However, current microarray imaging and analysis packages typically require manual intervention and assumptions on alignments. Unfortunately, limitations and assumptions are typically undisclosed and methods are not published. To facilitate exploration of image data, we developed SignalViewer. This paper presents a description of the application.

关键词： Artifacts Data Display image processing, computer-assisted/instrumentation image processing, computer-assisted/methods Internet Microarray Analysis/methods Software User-computer Interface

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A developer's commentary on fiswidgets

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NEUROINFORMATICS 2003年第1期1卷 131-133页

作者： Strother, SC Univ Minnesota Dept Radiol Minneapolis MN 55417 USA

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Mapping cortical gray matter asymmetry patterns in adolescents with heavy prenatal alcohol exposure

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NEUROimage 2002年第4期17卷 1807-1819页

作者： Sowell, ER Thompson, PM Peterson, BS Mattson, SN Welcome, SE Henkenius, AL Riley, EP Jernigan, TL Toga, AW Univ Calif Los Angeles Dept Neurol Lab Neuro Imaging Los Angeles CA 90095 USA Columbia Univ Coll Phys & Surg Dept Psychiat New York NY 10032 USA New York State Psychiat Inst & Hosp New York NY 10032 USA San Diego State Univ Ctr Behav Teratol San Diego CA 92120 USA Univ Calif San Diego Sch Med Dept Radiol La Jolla CA 92093 USA Univ Calif San Diego Sch Med Dept Psychiat La Jolla CA 92093 USA Univ Calif San Diego Sch Med Dept Vet Affairs Med Ctr La Jolla CA 92093 USA

Here we report on detailed three-dimensional quantitative maps of brain surface and gray matter density asymmetry patterns during normal adolescent development and show how these anatomical features of the brain are disrupted as a result of prenatal exposure to large quantities of alcohol. We studied two independent samples of normally developing children, adolescents, and young adults, totaling 83 subjects from two different research groups, and compared them to 21 individuals with heavy prenatal alcohol exposure. Surface-based image analysis techniques allowed us to match cortical anatomy across subjects and between hemispheres based on manually delineated sulcal landmarks. Quantitative maps of brain surface asymmetry reveal prominent peri-Sylvian hemispheric differences in which the superior temporal and inferior parietal cortices are shifted backward in the left relative to the right hemisphere in both normal and alcohol-exposed subjects. Cortical surface gray matter asymmetry, mapped here in adolescent populations, is most prominent in the posterior inferior temporal lobes (light greater than left), and this effect does not differ between groups of normally developing children, adolescents, or young adults. Alcohol-exposed individuals show a significant reduction in this asymmetry, whether studied with surface-based or more traditional volumetric region of interest analyses. This region of cortex, near the junction of Brodmann's areas 21, 22, and 37, primarily subserves language functions that are known to be impaired on average in the alcohol-exposed subjects. Our findings elucidate regional patterns of brain surface and gray matter asymmetry during normal development and may contribute to a more comprehensive understanding of the neural substrates of cognitive dysfunction after heavy prenatal alcohol exposure. (C) 2002 Elsevier Science (USA).

关键词： Adolescent Adult Brain Mapping/methods Brain Mapping/methods Cerebral Cortex/pathology Cerebral Cortex/physiopathology Child Dominance, Cerebral/physiology Female Fetal Alcohol Syndrome/diagnosis Fetal Alcohol Syndrome/pathology Fetal Alcohol Syndrome/physiopathology Humans image processing, computer-assisted/methods Imaging, Three-Dimensional/methods Magnetic Resonance Imaging/methods Male Pregnancy Reference Values

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The precision of anatomical normalization in the medial temporal lobe using spatial basis functions

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NEUROimage 2002年第1期17卷 507-512页

作者： Salmond, CH Ashburner, J Vargha-Khadem, F Connelly, A Gadian, DG Friston, KJ UCL Inst Child Hlth Dev Cognit Neurosci Unit London WC1N 1EM England UCL Inst Child Hlth Radiol & Phys Unit London WC1N 1EM England UCL Inst Neurol Wellcome Dept Imaging Neurosci London WC1N 1EM England

We investigated the accuracy of spatial basis function normalization using anatomical landmarks to determine how precisely homologous regions are colocalized. We examined precision in terms of. (1) the number of nonlinear basis functions used by the normalization procedure;(2) the degree of (Bayesian) regularization;and (3) the effect of substituting different templates and how this interacted with the number of basis functions. The face validity of spatial normalization was assessed as a function of these parameters, using the colocalization of homologous landmarks in a test sample of 20 normally developing children and 5 children with bilateral hippocampal pathology. Our results suggest that when optimal normalization parameters are used, anatomical landmarks in the medial temporal lobes are colocalized to within a standard deviation of about 1 mm. When suboptimal parameters are used this standard deviation can increase up to 3 mm. Interestingly the optimal parameters are those that provide a rather constrained normalization as opposed to those that optimize intensity matching at the expense of rendering the warps "unlikely." The implications of our results, for users of voxel-based morphometry, are discussed. (C) 2002 Elsevier Science (USA).

关键词： Adolescent Amnesia/pathology Child Female Functional Laterality/physiology Hippocampus/pathology Humans image processing, computer-assisted/methods Magnetic Resonance Imaging/methods Male Reproducibility of Results Temporal Lobe/anatomy & histology

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