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A component based noise correction method (CompCor) for BOLD and perfusion based fMRI

NEUROimage 2007年第1期37卷 90-101页

作者： Behzadi, Yashar Restom, Khaled Liau, Joy Liu, Thomas T. Univ Calif San Diego Ctr Funct Magnet Resonance Imaging La Jolla CA 92093 USA Univ Calif San Diego Dept Radiol La Jolla CA 92093 USA Univ Calif San Diego Dept Bioengn La Jolla CA 92093 USA

A component based method (CompCor) for the reduction of noise in both blood oxygenation level-dependent (BOLD) and perfusion-based functional magnetic resonance imaging (fMRI) data is presented. In the proposed method, significant principal components are derived from noise regions-of-interest (ROI) in which the time series data are unlikely to be modulated by neural activity. These components are then included as nuisance parameters within general linear models for BOLD and perfusion-based fMRI time series data. Two approaches for the determination of the noise ROI are considered. The first method uses high-resolution anatomical data to define a region of interest composed primarily of white matter and cerebrospinal fluid, while the second method defines a region based upon the temporal standard deviation of the time series data. With the application of CompCor, the temporal standard deviation of resting-state perfusion and BOLD data in gray matter regions was significantly reduced as compared to either no correction or the application of a previously described retrospective image based correction scheme (RETROICOR). For both functional perfusion and BOLD data, the application of CompCor significantly increased the number of activated voxels as compared to no correction. In addition, for functional BOLD data, there were significantly more activated voxels detected with CompCor as compared to RETROICOR. In comparison to RETROICOR, CompCor has the advantage of not requiring external monitoring of physiological fluctuations. (c) 2007 Elsevier Inc. All rights reserved.

关键词： Adult Algorithms Artifacts Cerebral Cortex/blood supply Cerebral Cortex/physiology Energy Metabolism/physiology Fourier Analysis Fourier Analysis Humans image Enhancement/methods image processing, computer-assisted/methods Linear Models Magnetic Resonance Imaging/methods Oxygen/blood Photic Stimulation Principal Component Analysis Regional Blood Flow/physiology Software Visual Perception/physiology

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Estimation of errors introduced by confocal imaging into the data on segmentation gene expression in Drosophila

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BIOINFORMATICS 2009年第3期25卷 346-352页

作者： Myasnikova, Ekaterina Surkova, Svetlana Panok, Lena Samsonova, Maria Reinitz, John St Petersburg State Polytech Univ St Petersburg 195251 Russia SUNY Stony Brook Stony Brook NY 11794 USA

Motivation: Currently the confocal scanning microscopy of fluorescently tagged molecules is extensively employed to acquire quantitative data on gene expression at cellular resolution. Following this approach, we generated a large dataset on the expression of segmentation genes in the Drosophila blastoderm, that is widely used in systems biology studies. As data accuracy is of critical importance for the success of studies in this field, we took a shot to evaluate possible errors introduced in the data by acquisition and processing methods. This article deals with errors introduced by confocal microscope. Results: In confocal imaging, the inevitable photon noise is commonly reduced by the averaging of multiple frames. The averaging may introduce errors into the data, if single frames are clipped by microscope hardware. A method based on censoring technique is used to estimate and correct this type of errors. Additional source of errors is the quanti. cation of blurred images. To estimate and correct these errors, the Richardson-Lucy deconvolution method was modified to provide the higher accuracy of data read off from blurred images of the Drosophila blastoderm. We have found that the sizes of errors introduced by confocal imaging make up similar to 5-7% of the mean intensity values and do not disguise the dynamic behavior and characteristic features of gene expression patterns. We also defined a range of microscope parameters for the acquisition of sufficiently accurate data.

关键词： Animals Blastoderm/metabolism Drosophila/genetics Drosophila/metabolism Gene Expression Gene Expression Profiling/methods Genes, Insect image processing, computer-assisted/methods Microscopy, Confocal/methods Regression Analysis

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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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Detecting change in BOLD signal between sessions for atlas-based anatomical ROIs

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NEUROimage 2008年第3期40卷 1157-1165页

作者： Buck, Robert Singhal, Harsh Arora, Jagriti Schlitt, Heidi Constable, R. Todd Pfizer Inc Ann Arbor MI USA Yale Univ MRCC New Haven CT USA Amgen Inc Thousand Oaks CA 91320 USA

An algorithm using pre-defined regions of interest (ROIs) to detect differences between sessions in Blood Oxygen-Level Dependent (BOLD) signal is proposed and results from a reproducibility study are reported here. It is important to know whether tests for change have the desired statistical properties, e. g., low variability between sessions and unbiased false-positive rates, under null conditions so one is confident in any conclusions based on the metric and test used. This study examined three cognitive tasks: Stroop, response inhibition, Sternberg digits, and a visually-cued finger tapping task, in 20 healthy subjects. Each subject had two fMRI sessions, one week apart. A series of ROI summaries was constructed by choosing different proportions of voxels from the ROI and calculating the mean of t values for the selected voxels. The choice of voxels was based on the magnitude of the t values, selecting the maximum value, then the top 1%, and so on until all voxels in the ROI were included. No ROIs were found to have significant differences between sessions based on paired comparison t tests. Generally, the observed false-positive rates were near the expected rates for all summaries and tasks, although the Sternberg and Response Inhibition tasks did have higher false-positive rates when alpha >= 0.1 for some ROI summaries. This study indicates results are reproducible and also have the desired statistical properties under null conditions. (C) 2008 Elsevier Inc. All rights reserved.

关键词： Adolescent Adult Aged Algorithms Artifacts Brain/anatomy & histology False Positive Reactions Female Humans image processing, computer-assisted/methods Magnetic Resonance Imaging/methods Magnetic Resonance Imaging/statistics & numerical data Male Middle Aged Neuropsychological Tests Oxygen/blood Psychomotor Performance/physiology Reproducibility of Results

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Integrating VBM into the general linear model with voxelwise anatomical covariates

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NEUROimage 2007年第2期34卷 500-508页

作者： Oakes, Terrence R. Fox, Andrew S. Johnstone, Tom Chung, Moo K. Kalin, Ned Davidson, Richard J. Univ Wisconsin Waisman Ctr Waisman Lab Brain Imaging & Behav Madison WI 53705 USA Univ Wisconsin Dept Psychol Madison WI 53706 USA Univ Wisconsin Dept Stat Madison WI 53706 USA Univ Wisconsin Dept Psychiat Madison WI 53706 USA

A current limitation for imaging of brain function is the potential confound of anatomical differences or registration error, which may manifest via apparent functional "activation" for between-subject analyses. With respect to functional activations, underlying tissue mismatches can be regarded as a nuisance variable. We propose adding the probability of gray matter at a given voxel as a covariate (nuisance variable) in the analysis of voxelwise multisubject functional data using standard statistical techniques. A method is presented to assess the extent to which a functional activation can reliably be explained by underlying anatomical differences, and simultaneously, to assess the component of the functional activation which cannot be attributed to anatomical difference and thus is likely due to functional difference alone. Extension of the method to other intermodal imaging applications is discussed. Two exemplary data sets, one PET and one fMRI, are used to demonstrate the implementation and utility of this method, which apportions the relative contributions of anatomy and function for an apparent functional activation. The examples show two distinct types of results. First, a so-called functional activation may actually be caused by a systematic anatomical difference which, when modeled, diminishes the functional effect. In the second result type, including the anatomical differences in the model can account for a large component of otherwise unmodeled variance, yielding an increase in the functional effect cluster size and/or magnitude. In either case, ignoring the readily available structural information can lead to misinterpretation of functional results. (c) 2006 Elsevier Inc. All rights reserved.

关键词： Brain/anatomy & histology Brain Mapping Brain Mapping Diagnostic Imaging Humans image processing, computer-assisted/methods Magnetic Resonance Imaging Positron-Emission Tomography

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Integration of touch and sound in auditory cortex

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NEURON 2005年第2期48卷 373-384页

作者： Kayser, C Petkov, CI Augath, M Logothetis, NK Max Planck Inst Biol Cybernet D-72076 Tubingen Germany

To form a coherent percept of the environment, our brain combines information from different senses. Such multisensory integration occurs in higher association cortices;but supposedly, it also occurs in early sensory areas. Confirming the latter hypothesis, we unequivocally demonstrate supra-additive integration of touch and sound stimulation at the second stage of the auditory cortex. Using high-resolution fMRI of the macaque monkey, we quantified the integration of auditory broad-band noise and tactile stimulation of hand and foot in anaesthetized animals. Integration was found posterior to and along the lateral side of the primary auditory cortex in the caudal auditory belt. Integration was stronger for temporally coincident stimuli and obeyed the principle of inverse effectiveness: greater enhancement for less effective stimuli. These findings demonstrates that multisensory integration occurs early and close to primary sensory areas and-because it occurs in anaesthetized animals-suggests that this integration is mediated by preattentive bottom-up mechanisms.

关键词： Animals Auditory Cortex/blood supply Auditory Cortex/physiology Auditory Perception/physiology Behavior, Animal Brain Mapping Brain Mapping image processing, computer-assisted/methods Macaca mulatta Magnetic Resonance Imaging/methods Oxygen/blood Physical Stimulation/methods Sound Sound Touch/physiology

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Is it tonotopy after all?

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NEUROimage 2002年第3期17卷 1144-1161页

作者： Schönwiesner, M von Cramon, DY Rübsamen, R Univ Leipzig Fac Biosci Pharm & Psychol D-04103 Leipzig Germany Max Planck Inst Cognit Neurosci Leipzig Germany

In this functional MRI study the frequency-dependent localization of acoustically evoked BOLD responses within the human auditory cortex was investigated. A blocked design was employed, consisting of periods of tonal stimulation (random frequency modulations with center frequencies 0.25, 0.5, 4.0, and 8.0 kHz) and resting periods during which only the ambient scanner noise was audible. Multiple frequency-dependent activation sites were reliably demonstrated on the surface of the auditory cortex. The individual gyral pattern of the superior temporal plane (STP), especially the anatomy of Heschl's gyros (HG), was found to be the major source of interindividual. variability. Considering this variability by tracking the frequency responsiveness to the four stimulus frequencies along individual Heschl's gyri yielded medio-lateral gradients of responsiveness to high frequencies medially and low frequencies laterally. It is, however, argued that with regard to the results of electrophysiological and cytoarchitectonical studies in humans and in nonhuman primates, the multiple frequency-dependent activation sites found in the present study as well as in other recent fMRI investigations are no direct indication of tonotopic organization of cytoarchitectonical areas. An alternative interpretation is that the activation sites correspond to different cortical fields, the topological organization of which cannot be resolved with the current spatial resolution of fMRI. In this notion, the detected frequency selectivity of different cortical areas arises from an excess of neurons engaged in the processing of different acoustic features, which are associated with different frequency bands. Differences in the response properties of medial compared to lateral and frontal compared to occipital portions of HG strongly support this notion. (C) 2002 Elsevier Science (USA).

关键词： Adult Artifacts Auditory Cortex/physiology Auditory Pathways/physiology Brain Mapping/methods Brain Mapping/methods Cerebral Cortex/physiology Female Humans image processing, computer-assisted/methods Imaging, Three-Dimensional Magnetic Resonance Imaging/methods Male Oxygen/blood Pitch Perception/physiology Psychoacoustics Sound Spectrography

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Linked independent component analysis for multimodal data fusion

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NEUROimage 2011年第3期54卷 2198-2217页

作者： Groves, Adrian R. Beckmann, Christian F. Smith, Steve M. Woolrich, Mark W. Univ Oxford FMRIB Ctr Funct MRI Brain Dept Clin Neurol Oxford OX1 2JD England Radboud Univ Nijmegen Donders Inst Brain Cognit & Behav Ctr Cognit Neuroimaging Nijmegen Netherlands Univ Twente MIRA Inst Biomed Technol & Tech Med Enschede Netherlands Univ Oxford OHBA Ctr Human Brain Act Dept Psychiat Oxford OX1 2JD England

In recent years, neuroimaging studies have increasingly been acquiring multiple modalities of data and searching for task-or disease-related changes in each modality separately. A major challenge in analysis is to find systematic approaches for fusing these differing data types together to automatically find patterns of related changes across multiple modalities, when they exist. Independent Component Analysis (ICA) is a popular unsupervised learning method that can be used to find the modes of variation in neuroimaging data across a group of subjects. When multimodal data is acquired for the subjects, ICA is typically performed separately on each modality, leading to incompatible decompositions across modalities. Using a modular Bayesian framework, we develop a novel "Linked ICA" model for simultaneously modelling and discovering common features across multiple modalities, which can potentially have completely different units, signal- and contrast-to-noise ratios, voxel counts, spatial smoothnesses and intensity distributions. Furthermore, this general model can be configured to allow tensor ICA or spatially-concatenated ICA decompositions, or a combination of both at the same time. Linked ICA automatically determines the optimal weighting of each modality, and also can detect single-modality structured components when present. This is a fully probabilistic approach, implemented using Variational Bayes. We evaluate the method on simulated multimodal data sets, as well as on a real data set of Alzheimer's patients and age-matched controls that combines two very different types of structural MRI data: morphological data (grey matter density) and diffusion data (fractional anisotropy, mean diffusivity, and tensor mode). (C) 2010 Elsevier Inc. All rights reserved.

关键词： Algorithms Alzheimer Disease/pathology Anisotropy Bayes Theorem Brain/pathology Data Interpretation, Statistical Diffusion Tensor Imaging Diffusion Tensor Imaging Humans image processing, computer-assisted/methods Models, Neurological Models, Statistical Principal Component Analysis

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A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells

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BIOINFORMATICS 2001年第12期17卷 1213-1223页

作者： Boland, MV Murphy, RF Carnegie Mellon Univ Dept Biol Sci Pittsburgh PA 15213 USA Ctr Light Microscope Imaging & Biotechnol Biomed & Hlth Engn Program Pittsburgh PA 15213 USA

Motivation: Assessment of protein subcellular location is crucial to proteomics efforts since localization information provides a context for a protein's sequence, structure, and function. The work described below is the first to address the subcellular localization of proteins in a quantitative., comprehensive manner. Results: images for ten different subcellular patterns (including all major organelles) were collected Using fluorescence microscopy. The patterns were described using a variety of numeric features, including Zernike moments, Haralick texture features, and a set, of new features developed specifically for this purpose. To test the usefulness of these features, they were used to train a neural network classifier. The classifier was able to correctly recognize an average of 83% of previously unseen cells showing one of the ten patterns. The same classifier was then used to recognize previously unseen sets of homogeneously prepared cells with 98% accuracy.

关键词： Algorithms Hela Cells Humans image processing, computer-assisted/methods Microscopy, Fluorescence/methods Neural Networks (computer) Proteins/analysis Subcellular Fractions/chemistry

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Partial volume corrected image derived input functions for dynamic PET brain studies:: Methodology and validation for [¹¹C] flumazenil

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NEUROimage 2008年第3期39卷 1041-1050页

作者： Mourik, Jurgen E. M. Lubberink, Mark Klumpers, Ursula M. H. Comans, Emile F. Lammertsma, Adriaan A. Boellaard, Ronald Vrije Univ Amsterdam Med Ctr Dept Nucl Med & PET Res NL-1007 MB Amsterdam Netherlands Vrije Univ Amsterdam Med Ctr Dept Psychiat Amsterdam Netherlands

Extraction of arterial input functions from dynamic brain scans may obviate the need for arterial sampling and would increase the clinical applicability of quantitative PET studies. The aim of the present study was to evaluate applicability and accuracy of image derived input functions (IDIFs) following reconstruction based partial volume correction (PVC). Settings for the PVC ordered subset expectation maximization (PVC-OSEM) reconstruction algorithm were varied. In addition, different methods for defining arterial regions of interest (1101) in order to extract IDIFs were evaluated. [C-11]flumazenil data of 10 subjects were used in the present study. Results obtained with IDIFs were compared with those using standard on-line measured arterial input functions. These included areas under the curve (AUC) for peak (1-2 min) and tail (2-60 min), volume of distribution (V-T) obtained using Logan analysis, and VT and K, obtained with a basis function implementation of a single tissue compartment model. Best results were obtained with PVC-OSEM using 4 iterations and 16 subsets. Based on 11 C point source measurements, a 4.5 non FWHM (full width at half maximum) resolution kernel was used to correct for partial volume effects. A ROI consisting of the four hottest pixels per plane (over the carotid arteries) was the best method to extract IDIFs. Excellent peak AUC ratios (0.99 +/- 0.09) between IDIF and blood sampler input function (BSIF) were found. Furthermore, extracted IDIFs provided V-T, and K-1 values that were very similar to those obtained using BSIFs. The proposed method appears to be suitable for analysing [C-11] flumazenil data without the need for online arterial sampling. (c) 2007 Elsevier Inc. All rights reserved.

关键词： Area Under Curve Brain/radionuclide imaging Calibration Carotid Arteries/radionuclide imaging Flumazenil/diagnostic use Flumazenil/pharmacokinetics Fourier Analysis Fourier Analysis GABA Modulators/diagnostic use GABA Modulators/pharmacokinetics Humans image processing, computer-assisted/methods Radiopharmaceuticals/diagnostic use Radiopharmaceuticals/diagnostic use Radiopharmaceuticals/pharmacokinetics Radiopharmaceuticals/pharmacokinetics

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