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Evaluation of volume-based and surface-based brain image registration methods

NEUROimage 2010年第1期51卷 214-220页

作者： Klein, Arno Ghosh, Satrajit S. Avants, Brian Yeo, B. T. T. Fischl, Bruce Ardekani, Babak Gee, James C. Mann, J. J. Parsey, Ramin V. Columbia Univ New York State Psychiat Inst New York NY 10032 USA MIT Elect Res Lab Cambridge MA 02139 USA Univ Penn Dept Radiol Penn Image Comp & Sci Lab Philadelphia PA 19104 USA Harvard Univ Cognit Neurosci Lab Cambridge MA 02138 USA Massachusetts Gen Hosp Athinoula A Martinos Ctr Boston MA 02114 USA Harvard Univ Sch Med Dept Radiol Cambridge MA 02138 USA MIT CSAIL Cambridge MA 02139 USA Nathan S Kline Inst Psychiat Res Orangeburg NY 10962 USA NYU Sch Med New York NY 10016 USA

Establishing correspondences across brains for the purposes of comparison and group analysis is almost universally done by registering images to one another either directly or via a template. However, there are many registration algorithms to choose from. A recent evaluation of fully automated nonlinear deformation methods applied to brain image registration was restricted to volume-based methods. The present study is the first that directly compares some of the most accurate of these volume registration methods with surface registration methods, as well as the first study to compare registrations of whole-head and brain-only (de-skulled) images. We used permutation tests to compare the overlap or Hausdorff distance performance for more than 16,000 registrations between 80 manually labeled brain images. We compared every combination of volume-based and surface-based labels, registration, and evaluation. Our primary findings are the following: 1. de-skulling aids volume registration methods;2. custom-made optimal average templates improve registration over direct pairwise registration;and 3. resampling volume labels on surfaces or converting surface labels to volumes introduces distortions that preclude a fair comparison between the highest ranking volume and surface registration methods using present resampling methods. From the results of this study, we recommend constructing a custom template from a limited sample drawn from the same or a similar representative population, using the same algorithm used for registering brains to the template. (C) 2010 Published by Elsevier Inc.

关键词： Adult Algorithms Brain/anatomy & histology Female Head/anatomy & histology Humans image processing, computer-assisted/methods Imaging, Three-Dimensional/methods Magnetic Resonance Imaging/methods Male Organ Size Software Young Adult

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Superresolution Imaging of Chemical Synapses in the Brain

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NEURON 2010年第5期68卷 843-856页

作者： Dani, Adish Huang, Bo Bergan, Joseph Dulac, Catherine Zhuang, Xiaowei Harvard Univ Howard Hughes Med Inst Cambridge MA 02138 USA Harvard Univ Dept Mol & Cellular Biol Cambridge MA 02138 USA Harvard Univ Dept Phys Dept Chem & Chem Biol Cambridge MA 02138 USA

Determination of the molecular architecture of synapses requires nanoscopic image resolution and specific molecular recognition, a task that has so far defied many conventional imaging approaches. Here, we present a superresolution fluorescence imaging method to visualize the molecular architecture of synapses in the brain. Using multicolor, three-dimensional stochastic optical reconstruction microscopy, the distributions of synaptic proteins can be measured with nanometer precision. Furthermore, the wide-field, volumetric imaging method enables high-throughput, quantitative analysis of a large number of synapses from different brain regions. To demonstrate the capabilities of this approach, we have determined the organization of ten protein components of the presynaptic active zone and the postsynaptic density. Variations in synapse morphology, neurotransmitter receptor composition, and receptor distribution were observed both among synapses and across different brain regions. Combination with optogenetics further allowed molecular events associated with synaptic plasticity to be resolved at the single-synapse level.

关键词： Animals Brain/metabolism Brain/ultrastructure Brain Chemistry/physiology image processing, computer-assisted/instrumentation image processing, computer-assisted/methods Imaging, Three-Dimensional/instrumentation Imaging, Three-Dimensional/methods Immunohistochemistry/methods Immunohistochemistry/methods Mice Mice, Inbred C57BL Microchemistry/methods Microscopy, Fluorescence/instrumentation Microscopy, Fluorescence/methods Molecular Imaging/instrumentation Molecular Imaging/methods Nanotechnology Nerve Tissue Proteins/metabolism Nerve Tissue Proteins/ultrastructure Neuronal Plasticity/physiology Photomicrography/instrumentation Photomicrography/methods Presynaptic Terminals/metabolism Presynaptic Terminals/ultrastructure Stochastic Processes Synapses/metabolism Synapses/ultrastructure

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Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing

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BIOINFORMATICS 2010年第12期26卷 i7-i12页

作者： Coelho, Luis Pedro Peng, Tao Murphy, Robert F. Carnegie Mellon Univ Lane Ctr Computat Biol Pittsburgh PA 15213 USA Carnegie Mellon Univ Ctr Bioimage informat Pittsburgh PA 15213 USA Carnegie Mellon Univ Joint Carnegie Mellon Univ Univ Pittsburgh Ph D Program Computat Biol Pittsburgh PA 15213 USA Carnegie Mellon Univ Dept Biomed Engn Pittsburgh PA 15213 USA Carnegie Mellon Univ Dept Biol Sci Pittsburgh PA 15213 USA Carnegie Mellon Univ Dept Machine Learning Pittsburgh PA 15213 USA Univ Freiburg Freiburg Inst Adv Studies D-79104 Freiburg Germany

Motivation: Proteins exhibit complex subcellular distributions, which may include localizing in more than one organelle and varying in location depending on the cell physiology. Estimating the amount of protein distributed in each subcellular location is essential for quantitative understanding and modeling of protein dynamics and how they affect cell behaviors. We have previously described automated methods using fluorescent microscope images to determine the fractions of protein fluorescence in various subcellular locations when the basic locations in which a protein can be present are known. As this set of basic locations may be unknown (especially for studies on a proteome-wide scale), we here describe unsupervised methods to identify the fundamental patterns from images of mixed patterns and estimate the fractional composition of them. methods: We developed two approaches to the problem, both based on identifying types of objects present in images and representing patterns by frequencies of those object types. One is a basis pursuit method (which is based on a linear mixture model), and the other is based on latent Dirichlet allocation (LDA). For testing both approaches, we used images previously acquired for testing supervised unmixing methods. These images were of cells labeled with various combinations of two organelle-specific probes that had the same fluorescent properties to simulate mixed patterns of subcellular location. Results: We achieved 0.80 and 0.91 correlation between estimated and underlying fractions of the two probes (fundamental patterns) with basis pursuit and LDA approaches, respectively, indicating that our methods can unmix the complex subcellular distribution with reasonably high accuracy.

关键词： Algorithms Fluorescent Dyes/analysis image processing, computer-assisted/methods Proteins/analysis Proteins/chemistry Subcellular Fractions/metabolism Subcellular Fractions/ultrastructure

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Hematopoiesis in 3 dimensions: human and murine bone marrow architecture visualized by confocal microscopy

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BLOOD 2010年第15期116卷 E41-E55页

作者： Takaku, Tomoiku Malide, Daniela Chen, Jichun Calado, Rodrigo T. Kajigaya, Sachiko Young, Neal S. NHLBI Hematol Branch NIH Bethesda MD 20892 USA NHLBI Light Microscopy Core Facil NIH Bethesda MD 20892 USA

In many animals, blood cell production occurs in the bone marrow. Hematopoiesis is complex, requiring self-renewing and pluripotent stem cells, differentiated progenitor and precursor cells, and supportive stroma, adipose tissue, vascular structures, and extracellular matrix. Although imaging is a vital tool in hematology research, the 3-dimensional architecture of the bone marrow tissue in situ remains largely uncharacterized. The major hindrance to imaging the intact marrow is the surrounding bone structures are almost impossible to cut/image through. We have overcome these obstacles and describe a method whereby whole-mounts of bone marrow tissue were immunostained and imaged in 3 dimensions by confocal fluorescence and reflection microscopy. We have successfully mapped by multicolor immunofluorescence the localization pattern of as many as 4 cell features simultaneously over large tiled views and to depths of approximately 150 mu m. Three-dimensional images can be assessed qualitatively and quantitatively to appreciate the distribution of cell types and their interrelationships, with minimal perturbations of the tissue. We demonstrate its application to normal mouse and human marrow, to murine models of marrow failure, and to patients with aplastic anemia, myeloid, and lymphoid cell malignancies. The technique should be generally adaptable for basic laboratory investigation and for clinical diagnosis of hematologic diseases. (Blood.2010;116(15):e41-e55)

关键词： Anemia, Aplastic/pathology Animals Bone Marrow/anatomy & histology Bone Marrow/pathology Bone Marrow Transplantation Female Green Fluorescent Proteins/genetics Hematologic Diseases/pathology Hematopoiesis Humans image processing, computer-assisted/methods Imaging, Three-Dimensional/methods Male Mice Mice, Congenic Mice, Inbred Strains Mice, Transgenic Mice, Transgenic Microscopy, Confocal/methods

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Preserved Functional Specialization for Spatial processing in the Middle Occipital Gyrus of the Early Blind

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NEURON 2010年第1期68卷 138-148页

作者： Renier, Laurent A. Anurova, Irina De Volder, Anne G. Carlson, Synnove VanMeter, John Rauschecker, Josef P. Georgetown Univ Med Ctr Dept Physiol & Biophys Lab Integrat Neurosci & Cognit Washington DC 20007 USA Catholic Univ Louvain Inst Neurosci B-1200 Brussels Belgium Univ Helsinki Inst Biomed Physiol Neurosci Unit FIN-00014 Helsinki Finland Aalto Univ Sch Sci & Technol Low Temp Lab Brain Res Unit FI-00076 Aalto Finland Univ Tampere Sch Med Tampere 33014 Finland Georgetown Univ Med Ctr Ctr Funct & Mol Imaging Washington DC 20007 USA Aalto Univ Sch Sci & Technol Ctr Excellence Computat Complex Syst Res Mind & Brain Lab FI-00076 Aalto Finland

The occipital cortex (OC) of early-blind humans is activated during various nonvisual perceptual and cognitive tasks, but little is known about its modular organization. Using functional MRI we tested whether processing of auditory versus tactile and spatial versus nonspatial information was dissociated in the OC of the early blind. No modality-specific OC activation was observed. However, the right middle occipital gyrus (MOG) showed a preference for spatial over nonspatial processing of both auditory and tactile stimuli. Furthermore, MOG activity was correlated with accuracy of individual sound localization performance. In sighted controls, most of extrastriate OC, including the MOG, was deactivated during auditory and tactile conditions, but the right MOG was more activated during spatial than nonspatial visual tasks. Thus, although the sensory modalities driving the neurons in the reorganized OC of blind individuals are altered, the functional specialization of extrastriate cortex is retained regardless of visual experience.

关键词： Acoustic Stimulation/methods Adult Analysis of Variance Blindness/pathology Blindness/physiopathology Brain Mapping Brain Mapping Case-Control Studies Female Humans image processing, computer-assisted/methods Magnetic Resonance Imaging/methods Male Middle Aged Occipital Lobe/blood supply Occipital Lobe/physiopathology Oxygen/blood Sound Localization/physiology Space Perception/physiology Touch/physiology

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Joint analysis of structural and perfusion MRI for cognitive assessment and classification of Alzheimer's disease and normal aging

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NEUROimage 2010年第1期52卷 186-197页

作者： Tosun, Duygu Mojabi, Pouria Weiner, Michael W. Schuff, Norbert Dept Vet Afrairs Med Ctr Ctr Imaging Neurodegenerat Dis San Francisco CA 94121 USA Univ Calif San Francisco Dept Radiol San Francisco CA 94143 USA

Structural magnetic resonance imaging (MRI) of brain tissue loss and physiological imaging of regional cerebral blood flow (rCBF) can provide complimentary information for the characterization of brain disorders, such as Alzheimer's disease (AD) but studies into gains in classification power for AD using these image modalities Jointly have been limited Our aim in this study was to determine the Joint contribution of structural and perfusion-weighted imaging for the classification of AD in a cross-sectional study using an integrated multimodality MRI processing framework and a cortical surface-based analysis approach We used logistic regression analysis to determine sequentially the value of cortical thickness, rCBF, and cortical thickness and rCBF Jointly for classification for diagnosis of AD compared to controls We further tested the extent to which cortical thinning and reduced rCBF explain individually or together variability in dementia severity Separate analysis of structural MRI and perfusion-weighted MRI data yielded the well-established pattern of cortical thinning and rCBF reduction in AD, affecting predominantly temporo-parietal brain regions Using structural MRI and perfusion-weighted MRI Jointly indicated that cortical thinning dominated the classification of AD and controls without significant contributions from rCBF However there was also a positive interaction between reduced rCBF and cortical thinning in the right superior temporal sulcus, implying that structural and physiological brain alterations in AD can be complementary Compared to reduced rCBF, regional cortical thinning better explained the variability in dementia severity In conclusion, structural brain alterations compared to physiological variations are the dominant features of MRI in AD (C) 2010 Elsevier Inc All rights reserved.

关键词： Aged Aged, 80 and over Aging/pathology Aging/physiology Alzheimer Disease/pathology Alzheimer Disease/physiopathology Brain/blood supply Brain/pathology Brain/physiopathology Cerebral Cortex/parasitology Cerebral Cortex/pathology Cerebral Cortex/physiopathology Cerebrovascular Circulation Cognition/physiology Cross-Sectional Studies Female Humans image processing, computer-assisted/methods Logistic Models Magnetic Resonance Angiography/methods Magnetic Resonance Imaging/methods Male Middle Aged Organ Size Regional Blood Flow Severity of Illness Index Severity of Illness Index Signal processing, computer-assisted

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An analysis of image texture, tumor location, and MGMT promoter methylation in glioblastoma using magnetic resonance imaging

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NEUROimage 2010年第2期49卷 1398-1405页

作者： Drabycz, Sylvia Roldan, Gloria de Robles, Paula Adler, Daniel McIntyre, John B. Magliocco, Anthony M. Cairncross, J. Gregory Mitchell, J. Ross Univ Calgary Dept Elect & Comp Engn Calgary AB T2N 1N4 Canada Hotchkiss Brain Inst Calgary AB Canada Univ Calgary Dept Clin Neurosci Calgary AB T2N 1N4 Canada Univ Calgary Dept Pathol & Lab Med Calgary AB T2N 1N4 Canada Univ Calgary Dept Radiol Calgary AB T2N 1N4 Canada

In glioblastoma (GBM), promoter methylation of the DNA repair gene O-6-methylguanine-DNA methyltransferase (MGMT) is associated with benefit from chemotherapy. Correlations between MGMT promoter methylation and visually assessed imaging features on magnetic resonance (MR) have been reported suggesting that noninvasive detection of MGMT methylation status might be possible. Our study assessed whether MGMT methylation status in GBM could be predicted using MR imaging. We conducted a retrospective analysis of MR images in patients with newly diagnosed GBM. Tumor texture was assessed by two methods. First, we analyzed texture by expert consensus describing the tumor borders, presence or absence of cysts, pattern of enhancement, and appearance of tumor signal in T2-weighted images. Then, we applied space-frequency texture analysis based on the S-transform. Tumor location within the brain was determined using automatized image registration and segmentation techniques. Their association with MGMT methylation was analyzed. We confirmed that ring enhancement assessed visually is significantly associated with unmethylated MGMT promoter status (P = 0.006). Texture features on T2-weighted images assessed by the space-frequency analysis were significantly different between methylated and unmethylated cases (P<0.05). However, blinded classification of MGMT promoter methylation status reached an accuracy of only 71%. There were no significant differences in the locations of methylated and unmethylated GBM tumors. Our results provide further evidence that individual MR features are associated with MGMT methylation but better algorithms for predicting methylation status are needed. The relevance of this study lies on the application of novel techniques for the analysis of anatomical MR images of patients with GBM allowing the evaluation of subtleties not seen by an observer and facilitating the standardization of the methods, decreasing the potential for interobserver bias. (C) 2009

关键词： Adult Aged Aged, 80 and over Brain/metabolism Brain/pathology Brain Neoplasms/metabolism Brain Neoplasms/pathology DNA Methylation DNA Modification Methylases/genetics DNA Modification Methylases/metabolism DNA Repair Enzymes/genetics DNA Repair Enzymes/metabolism Female Glioblastoma/metabolism Glioblastoma/pathology Humans image processing, computer-assisted/methods Magnetic Resonance Imaging/methods Male Middle Aged Promoter Regions, Genetic Retrospective Studies Retrospective Studies Tumor Suppressor Proteins/genetics Tumor Suppressor Proteins/metabolism

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Whole brain quantitative T2 MRI across multiple scanners with dual echo FSE: Applications to AD, MCI, and normal aging

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NEUROimage 2010年第2期52卷 508-514页

作者： Bauer, Corinna M. Jara, Hernan Killiany, Ron Boston Univ Sch Med Dept Anat & Neurobiol Boston MA 02118 USA Boston Univ Sch Med Dept Radiol Boston Med Ctr Boston MA 02118 USA Boston Univ Dept Biomed Engn Boston MA 02215 USA Boston Univ Sch Med Ctr Biomed Imaging Boston MA 02118 USA Boston Univ Sch Publ Hlth Dept Environm Hlth Boston MA 02118 USA

The ability to pool data from multiple MRI scanners is becoming increasingly important with the influx in multi-site research studies. Fast spin echo (FSE) dual spin echo sequences are often chosen for such studies based principally on their short acquisition time and the clinically useful contrasts they provide for assessing gross pathology. The practicality of measuring FSE-T2 relaxation properties has rarely been assessed. Here, FSE-T2 relaxation properties are examined across the three main scanner vendors (General Electric (GE), Philips, and Siemens). The American College of Radiology (ACR) phantom was scanned on four 1.5 T platforms (two GE, one Philips, and one Siemens) to determine if the dual echo pulse sequence is susceptible to vendor-based variance. In addition, data from 85 subjects spanning the spectrum of normal aging, mild cognitive impairment (MCI), and Alzheimer's disease (AD) was obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI) to affirm the presence of any phantom based between vendor variance and determine the relationship between this variance and disease. FSE-T2 relaxation properties, including peak FSE-T2 and histogram width, were calculated for each phantom and human subject. Direct correspondence was found between the phantom and human subject data. Peak FSE-T2 of Siemens scanners was consistently at least 20 ms prolonged compared to GE and Philips. Siemens scanners showed broader FSE-T2 histograms than the other scanners. Greater variance was observed across GE scanners than either Philips or Siemens. FSE-T2 differences were much greater with scanner vendor than between diagnostic groups, as no significant changes in peak FSE-T2 or histogram width between normal aged, MCI, and AD subject groups were observed. These results indicate that whole brain histogram measures are not sensitive enough to detect FSE-T2 changes between normal aging, MCI, and AD and that FSE-T2 is highly variable across scanner vendors. (C) 2010 Els

关键词： Aged Aged, 80 and over Aging/pathology Algorithms Alzheimer Disease/pathology Brain/pathology Cognition Disorders/pathology Female Humans image processing, computer-assisted/instrumentation image processing, computer-assisted/methods Magnetic Resonance Imaging/instrumentation Magnetic Resonance Imaging/methods Male Middle Aged Phantoms, Imaging Severity of Illness Index Severity of Illness Index Time Factors

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Learning partially directed functional networks from meta-analysis imaging data

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NEUROimage 2010年第2期49卷 1372-1384页

作者： Neumann, Jane Fox, Peter T. Turner, Robert Lohmann, Gabriele Max Planck Inst Human Cognit & Brain Sci Dept Neurophys D-04103 Leipzig Germany Univ Texas Hlth Sci Ctr San Antonio Res Imaging Ctr San Antonio TX USA

We Propose a new exploratory method for the discovery of partially directed functional networks from fMRI meta-analysis data. The method performs structure learning of Bayesian networks in search of directed probabilistic dependencies between brain regions. Learning is based on the co-activation of brain regions observed across several independent imaging experiments. In a series of simulations, we first demonstrate the reliability of the method. We then present the application of our approach in an extensive meta-analysis including several thousand activation coordinates from more than 500 imaging studies. Results show that our method is able to automatically infer Bayesian networks that capture both directed and undirected probabilistic dependencies between a number of brain regions, including regions that are frequently observed in motor-related and cognitive control tasks. (C) 2009 Elsevier Inc. All rights reserved.

关键词： Artificial Intelligence Automation Bayes Theorem Brain/physiology Cluster Analysis computer Simulation Humans image processing, computer-assisted/methods Magnetic Resonance Imaging/methods Meta-Analysis as Topic Neural Pathways/physiology Probability

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Noninvasive visualization of human dopamine dynamics from PET images

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NEUROimage 2010年第1期51卷 135-144页

作者： Morris, E. D. Constantinescu, C. C. Sullivan, J. M. Normandin, M. D. Christopher, L. A. Indiana Univ Purdue Univ Dept Biomed Engn Indianapolis IN 46202 USA Purdue Univ Dept Biomed Engn W Lafayette IN 47907 USA Indiana Univ Sch Med Dept Radiol Indianapolis IN 46202 USA Univ Calif Irvine Dept Psychiat & Human Behav Irvine CA 92717 USA Indiana Univ Purdue Univ Dept Elect & Comp Engn Indianapolis IN 46202 USA

We recently introduced strategies for extracting temporal patterns of brain dopamine fluctuations from dynamic positron emission tomography (PET) data using the tracer [11C]-raclopride. Each of our methods yields a collection of time-concentration curves for endogenous dopamine. Given a spatially dense collection of curves (i.e., one at every voxel in a region of interest), we produce image volumes of dopamine (DA) concentration, DA( X, t), at multiple voxel locations and each time-frame. The volume over time-frames constitutes a 4D dataset that can be thought of as a DA "movie". There are a number of ways to visualize such data. Viewing cine loops of a slice through the DA volume is one way. Creating images of dopamine peak-time, T-peak(X), derived from a movie, is another. Each visualization may reveal spatio-temporal patterns of neurotransmitter activity heretofore unobservable. We conducted an initial validation experiment in which identical DA responses were induced by an identical task, initiated at different times by the same subject, in two separate PET scans. A comparison of the resulting T-peak(X) images revealed a large contiguous cluster of striatal voxels, on each side, whose DA timing was consistent with the relative timing of the tasks. Hence, the DA movies and their respective peak-time images were shown to be new types of functional images that contain bonafide timing information about a neurotransmitter's response to a stimulus. (C) 2009 Elsevier Inc. All rights reserved.

关键词： Algorithms Brain/metabolism Brain/radionuclide imaging Brain Mapping/methods Brain Mapping/methods Cluster Analysis Dopamine/metabolism Fingers/physiology Humans image processing, computer-assisted/methods Imaging, Three-Dimensional/methods Male Motor Activity/physiology Positron-Emission Tomography/methods Raclopride Raclopride Time Factors Video Recording

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