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Measuring the hemodynamic response in chronic hypoperfusion

NEUROCASE 2006年第3期12卷 146-150页

作者： Fridriksson, Julius Rorden, Chris Morgan, Paul S. Morrow, K. Leigh Baylis, Gordon C. Univ S Carolina Dept Commun Sci & Disorders Columbia SC 29208 USA Univ Nottingham Dept Acad Radiol Nottingham NG7 2RD England Univ S Carolina Dept Psychol Columbia SC 29208 USA Med Univ S Carolina Brain Imaging Ctr Excellence Columbia SC USA

Although structural brain scans help assess brain injury in stroke, they cannot identify regions that are functionally disabled due to disrupted perfusion. Perfusion and functional MRI have the potential for determining the functional consequences of stroke. Here we examine the effectiveness of functional MRI to measure brain function in a single patient (LB) with chronic hypoperfusion. When LB made sustained hand movements we observed a sustained decrease in the fMRI signal, while normal individuals exhibit a sustained increase in signal while conducting this task. This work has clear implications for understanding stroke using functional MRI.

关键词： Brain Injuries/pathology Brain Injuries/pathology Brain Injuries/physiopathology Brain Injuries/physiopathology Cerebral Cortex/blood supply Cerebral Cortex/pathology Functional Laterality/physiology Hemodynamics/physiology Humans image processing, computer-assisted/methods Magnetic Resonance Imaging/methods Male Middle Aged Oxygen/blood Stroke/physiopathology

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Development of a Noninvasive Method to Diagnose Bladder Outlet Obstruction Based on Decorrelation of Sequential Ultrasound images

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UROLOGY 2015年第3期85卷 648-652页

作者： Arif, Muhammad Idzenga, Tim de Korte, Chris L. van Mastrigt, Ron Erasmus MC Sect Furore Dept Urol NL-3015 GE Rotterdam Netherlands Radboud Univ Nijmegen Med Ctr Med UltraSound Imaging Ctr MUSIC Dept Radiol NL-6525 ED Nijmegen Netherlands

OBJECTIVE To develop an ultrasound (US)-based method for noninvasive diagnosing of bladder outlet obstruction, and the relationship between decorrelation of sequential US images and the degree of obstruction in a urethra model was studied. MATERIALS AND methods A flexible model of a male urethra was constructed from 15% aqueous solution of polyvinyl alcohol cryogel. To create 4 different degrees of obstruction, polyvinyl alcohol rings representing the prostate were placed around the model. Each model was perfused at different flow rates (1-15 mL/s) with an aqueous solution containing scattering particles mimicking urine. At each flow rate, 10 sequential US images were acquired. The average correlation coefficients between the images were calculated and plotted as a function of the degree of obstruction and the flow rate. RESULTS The average correlation decreased approximately linearly with an increase in the degree of obstruction. This decrease in correlation (decorrelation) might be due to turbulence caused by the obstruction. A higher degree of obstruction creates more turbulence and results in a higher decorrelation between sequential US images. CONCLUSION Quantification of the decorrelation between sequential US images may provide us with a new approach to noninvasively diagnose bladder outlet obstruction. (C) 2015 Elsevier Inc.

关键词： Diagnostic Techniques, Urological Humans image processing, computer-assisted/methods image processing, computer-assisted/statistics & numerical data Male Models, Anatomic Urinary Bladder Neck Obstruction/ultrasonography

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A study-specific fMRI normalization approach that operates directly on high resolution functional EPI data at 7 Tesla

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NEUROimage 2014年 100卷 710-714页

作者： Grabner, Gunther Poser, Benedikt A. Fujimoto, Kyoko Polimeni, Jonathan R. Wald, Lawrence L. Trattnig, Siegfried Toni, Ivan Barth, Markus Radboud Univ Nijmegen Donders Inst Brain Cognit & Behav Ctr Cognit Neuroimaging NL-6525 ED Nijmegen Netherlands Univ Duisburg Essen Erwin L Hahn Inst Magnet Resonance Imaging Essen Germany Massachusetts Gen Hosp Dept Radiol AA Martinos Ctr Charlestown MA USA Harvard MIT Div Hlth Sci Technol Cambridge MA USA Med Univ Vienna Dept Biomed Imaging & Image Guided Therapy MR Ctr Excellence Vienna Austria Univ Queensland Ctr Adv Imaging St Lucia Qld 4072 Australia Maastricht Univ Fac Psychol & Neurosci Dept Cognit Neurosci Maastricht Brain Imaging Ctr Maastricht Netherlands

Due to the availability of ultra-high field scanners and novel imaging methods, high resolution, whole brain functional MR imaging (fMRI) has become increasingly feasible. However, it is common to use extensive spatial smoothing to account for inter-subject anatomical variation when pooling over subjects. This reduces the spatial details of group level functional activation considerably, even when the original data was acquired with high resolution. In our study we used an accelerated 3D EPI sequence at 7 Tesla to acquire whole brain fMRI data with an isotropic spatial resolution of 1.1 mm which shows clear gray/white matter contrast due to the stronger T1 weighting of 3D EPI. To benefit from the high spatial resolution on the group level, we develop a study specific, high resolution anatomical template which is facilitated by the good anatomical contrast that is present in the average functional EPI images. Different template generations with increasing accuracy were created by using a hierarchical linear and stepwise non-linear registration approach. As the template is based on the functional data themselves no additional co-registration step with the usual T1-weighted anatomical data is necessary which eliminates a potential source of misalignment. To test the improvement of functional localization and spatial details we performed a group level analysis of a finger tapping experiment in eight subjects. The most accurate template shows better spatial localization - such as a separation of somatosensory and motor areas and of single digit activation - compared to the simple linear registration. The number of activated voxels is increased by a factor of 1.2, 2.5, and 3.1 for somatosensory, supplementary motor area, and dentate nucleus, respectively, for the functional contrast between left versus right hand. Similarly, the number of activated voxels is increased 1.4- and 2.4-fold for right little versus right index finger and left little versus left index finger, re

关键词： Adult Brain Mapping/instrumentation Brain Mapping/instrumentation Brain Mapping/methods Brain Mapping/methods Cerebral Cortex/physiology Data Interpretation, Statistical Echo-Planar Imaging/instrumentation Echo-Planar Imaging/methods Humans image processing, computer-assisted/methods Magnetic Resonance Imaging/instrumentation Magnetic Resonance Imaging/methods Psychomotor Performance/physiology

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The impact of gradient strength on in vivo diffusion MRI estimates of axon diameter

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NEUROimage 2015年 106卷 464-472页

作者： Huang, Susie Y. Nummenmaa, Aapo Witzel, Thomas Duval, Tanguy Cohen-Adad, Julien Wald, Lawrence L. McNab, Jennifer A. Harvard Univ Massachusetts Gen Hosp Sch Med Athinoula A Martinos Ctr Biomed ImagingDept Radi Boston MA 02138 USA Ecole Polytech Inst Biomed Engn Montreal PQ H3C 3A7 Canada MIT Harvard Mit Div Hlth Sci & Technol Cambridge MA 02139 USA Stanford Univ Dept Radiol Radiol Sci Lab Stanford CA 94305 USA

Diffusion magnetic resonance imaging (MRI) methods for axon diameter mapping benefit from higher maximum gradient strengths than are currently available on commercial human scanners. Using a dedicated high-gradient 3 T human MRI scanner with a maximum gradient strength of 300 mT/m, we systematically studied the effect of gradient strength on in vivo axon diameter and density estimates in the human corpus callosum. Pulsed gradient spin echo experiments were performed in a single scan session lasting approximately 2 h on each of three human subjects. The data were then divided into subsets with maximum gradient strengths of 77, 145, 212, and 293 mT/m and diffusion times encompassing short (16 and 25 ms) and long (60 and 94 ms) diffusion time regimes. A three-compartment model of intra-axonal diffusion, extra-axonal diffusion, and free diffusion in cerebrospinal fluid was fitted to the data using a Markov chain Monte Carlo approach. For the acquisition parameters, model, and fitting routine used in our study, it was found that higher maximum gradient strengths decreased the mean axon diameter estimates by two to three fold and decreased the uncertainty in axon diameter estimates by more than half across the corpus callosum. The exclusive use of longer diffusion times resulted in axon diameter estimates that were up to two times larger than those obtained with shorter diffusion times. Axon diameter and density maps appeared less noisy and showed improved contrast between different regions of the corpus callosum with higher maximum gradient strength. Known differences in axon diameter and density between the genu, body, and splenium of the corpus callosum were preserved and became more reproducible at higher maximum gradient strengths. Our results suggest that an optimal q-space sampling scheme for estimating in vivo axon diameters should incorporate the highest possible gradient strength. The improvement in axon diameter and density estimates that we demonstrate from in

关键词： Axons Corpus Callosum/anatomy & histology Diffusion Magnetic Resonance Imaging/methods Humans image processing, computer-assisted/methods Markov Chains Models, Statistical Monte Carlo Method

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A principal skeleton algorithm for standardizing confocal images of fruit fly nervous systems

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BIOINFORMATICS 2010年第8期26卷 1091-1097页

作者： Qu, Lei Peng, Hanchuan Howard Hughes Med Inst Ashburn VA 20147 USA

Motivation: The fruit fly (Drosophila melanogaster) is a commonly used model organism in biology. We are currently building a 3D digital atlas of the fruit fly larval nervous system (LNS) based on a large collection of fly larva GAL4 lines, each of which targets a subset of neurons. To achieve such a goal, we need to automatically align a number of high-resolution confocal image stacks of these GAL4 lines. One commonly employed strategy in image pattern registration is to first globally align images using an affine transform, followed by local non-linear warping. Unfortunately, the spatially articulated and often twisted LNS makes it difficult to globally align the images directly using the affine method. In a parallel project to build a 3D digital map of the adult fly ventral nerve cord (VNC), we are confronted with a similar problem. Results: We proposed to standardize a larval image by best aligning its principal skeleton (PS), and thus used this method as an alternative of the usually considered affine alignment. The PS of a shape was defined as a series of connected polylines that spans the entire shape as broadly as possible, but with the shortest overall length. We developed an automatic PS detection algorithm to robustly detect the PS from an image. Then for a pair of larval images, we designed an automatic image registration method to align their PSs and the entire images simultaneously. Our experimental results on both simulated images and real datasets showed that our method does not only produce satisfactory results for real confocal larval images, but also perform robustly and consistently when there is a lot of noise in the data. We also applied this method successfully to confocal images of some other patterns such as the adult fruit fly VNC and center brain, which have more complicated PS. This demonstrates the flexibility and extensibility of our method.

关键词： Algorithms Animals Cell Line Drosophila melanogaster/physiology Drosophila melanogaster/ultrastructure image processing, computer-assisted/methods Imaging, Three-Dimensional/methods Microscopy, Confocal/methods Nervous System/ultrastructure

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Automatic cortical sulcal parcellation based on surface principal direction flow field tracking

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NEUROimage 2009年第4期46卷 923-937页

作者： Li, Gang Guo, Lei Nie, Jingxin Liu, Tianming Univ Georgia Dept Comp Sci Athens GA 30602 USA Univ Georgia Bioimaging Res Ctr Athens GA 30602 USA Northwestern Polytech Univ Sch Automat Xian 710072 Peoples R China

The human cerebral cortex is a highly convoluted Structure composed of sulci and gyri, corresponding to the valleys and ridges of the cortical surface respectively. Automatic parcellation of the cortical surface into sulcal regions is of great importance in structural and functional mapping of the human brain. In this paper, a novel method is proposed for automatic Cortical sulcal parcellation based on the geometric characteristics of cortical surface including its principal curvatures and principal directions. This method is composed of two major steps: 1) employing the hidden Markov random field model (HMRF) and the expectation maximization (EM) algorithm on the maximum principal curvatures of the cortical surface for sulcal region segmentation, and 2) using a principal direction flow field tracking method on the cortical surface for sulcal basin segmentation. The flow field is obtained by diffusing the principal direction field on the cortical surface mesh. A unique feature of this method is that the automatic sulcal parcellation process is quite robust and efficient, and is independent of any external guidance Such as atlas-based warping. The method has been successfully applied to the inner cortical surfaces of twelve healthy human brain MR images. Both quantitative and qualitative evaluation results demonstrate the validity and efficiency of the proposed method. (C) 2009 Elsevier Inc. All rights reserved.

关键词： Algorithms Brain Mapping/methods Brain Mapping/methods Cerebral Cortex/anatomy & histology Humans image processing, computer-assisted/methods Magnetic Resonance Imaging Reproducibility of Results

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INTRACELLULAR-LOCALIZATION OF DRUGS IN CULTURED TUMOR-CELLS BY ION MICROSCOPY AND image-processing

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HISTOCHEMISTRY 1990年第4期93卷 397-400页

作者： BERRY, JP LESPINATS, G ESCAIG, F BOUMATI, P TLOUZEAU, S CAVELLIER, JF FAC MED CRETEIL INSERM SC27 F-94000 CRETEIL FRANCE INST RECH SCI CANC CNRS ER 278 F-94805 VILLEJUIF FRANCE

Several drugs, containing a halogen atom, F or Br, that are being used in antiviral or anticancer therapy, were studied for their localization in cultured cells by ion microanalysis. The association allows to reduce the exposure time to define the intracellular localization of the studied element. The topography of the cells is given by the image of the polyatomic ion 26CN-. The image of the distribution of 81Br- or 19F-, cooled in another color scale, can be superimposed, giving a polychromic image of the cell, thus showing the intracellular localization of the compound. MCF-7 tumor cells were cultured in the presence of pyrimidine derivatives. 5-Bromo-2''-deoxyuridine (BUdR) and 5-trifluorothymidine (F3TdR) were localized in the nucleus, 5-fluoro-2''-deoxyuridine (FudR) in the nucleus and only in some nucleoli. The method is simple and rapid, as compared with techniques using radiolabeled compounds, or with immunocytochemical techniques. It is possible to observe two different compounds in the same cell. It could be applied to other compounds containing a halogen atom.

关键词： Bromodeoxyuridine/analysis Cyanides/analysis Floxuridine/analysis Halogens/analysis Humans image processing, computer-assisted/methods Ions Microscopy/methods Thymidine/analogs & derivatives Trifluridine/analysis Tumor Cells, Cultured/analysis

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Reconstructing fragmented gel files created by model 377 DNA sequencers

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BIOTECHNIQUES 1998年第6期24卷 1004-1005页

作者： O'Brien, KM Schageman, JJ Evans, GA Garner, HR Univ Texas SW Med Ctr Eugene McDermott Ctr Human Growth & Dev Dallas TX 75235 USA

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NucleusJ: an imageJ plugin for quantifying 3D images of interphase nuclei

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BIOINFORMATICS 2015年第7期31卷 1144-1146页

作者： Poulet, Axel Arganda-Carreras, Ignacio Legland, David Probst, Aline V. Andrey, Philippe Tatout, Christophe Clermont Univ GRED INSERM U 1103UMR CNRS 6293 Aubiere France IJPB ERL CNRS 3559 UMR INRA AgroParisTech 1318 Versailles France Food Proc Engn & Microbiol UMR INRA AgroParisTech 782 Thiverval Grignon France Univ Paris 06 Sorbonne Univ UFR 927 Paris France

A Summary: NucleusJ is a simple and user-friendly imageJ plugin dedicated to the characterization of nuclear morphology and chromatin organization in 3D. Starting from image stacks, the nuclear boundary is delimited by combining the Otsu segmentation method with optimization of nuclear sphericity. Chromatin domains are segmented by partitioning the nucleus using a 3D watershed algorithm and by thresholding a contrast measure over the resulting regions. As output, NucleusJ quantifies 15 parameters including shape and size of nuclei as well as intra-nuclear objects and their position within the nucleus. A step-by-step documentation is available for self-training, together with data sets of nuclei with different nuclear organization.

关键词： Algorithms Cell Nucleus/genetics Humans image processing, computer-assisted/methods Imaging, Three-Dimensional/methods Interphase/genetics

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Cup-to-disc ratio: Ophthalmoscopy versus automated measurement in a general population - The Rotterdam Study

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OPHTHALMOLOGY 1999年第8期106卷 1597-1601页

作者： Wolfs, RCW Ramrattan, RS Hofman, A de Jong, PTVM Netherlands Ophthalm Res Inst NL-1100 AC Amsterdam Netherlands Erasmus Univ Dept Ophthalmol Rotterdam Netherlands Erasmus Univ Dept Epidemiol & Biostat NL-3000 DR Rotterdam Netherlands Univ Amsterdam Acad Med Ctr Dept Ophthalmol NL-1105 AZ Amsterdam Netherlands

Objective: To determine the correlations between ophthalmoscopic estimations and the measurements with a semiautomated image-analysis device of the vertical cup-to-disc ratio (VCDR) in the human optic disc. Designs Population-based, cross-sectional study. Participants: All subjects 55 years of age and older from the population-based sample of 6777 ophthalmologically examined subjects from The Rotterdam Study of whom gradable optic disc transparencies of at least 1 eye and ophthalmoscopic data of the same eye were available. Main Outcome Measures: Ophthalmoscopic assessment of the VCDR and semiautomated measurement of the VCDR. methods: Indirect and direct ophthalmoscopy were performed in mydriasis to assess the VCDR, Optic disc transparencies made with a simultaneous stereoscopic telecentric fundus camera were analyzed with a semiautomated measurement system (Topcon imagenet). Results: In 5143 subjects, the mean ophthalmoscopic VCDR was 0.30 (standard error [SE], 0.0021;range, 0.00, 1.00) compared with a semiautomatically measured VCDR of 0.49 (SE, 0.0019;range, 0.04, 0.86;difference, 0.19;P < 0.0001). The overall correlation between both methods was moderate (correlation coefficient, 0.61;SE, 0.11) and lower in small optic discs. Semiautomated optic disc measurements correctly identified 76% of the glaucoma cases las defined using visual field data and ophthalmoscopic data about the optic disc). Conclusion: Semiautomated measurements of the VCDR are larger than the ophthalmoscopic VCDR estimate with a moderate correlation. The interobserver variability using imagenet was smaller compared with the ophthalmoscopic assessments, and imagenet was better standardized, which is important for epidemiologic surveys and follow-up studies.

关键词： Aged Aged, 80 and over Cohort Studies Cross-Sectional Studies Female Glaucoma, Open-Angle/diagnosis Humans image processing, computer-assisted/methods Male Middle Aged Netherlands Observer Variation Ophthalmoscopy/methods Optic Disk/pathology Photography Reproducibility of Results

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