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      PRoNTo: Pattern Recognition for Neuroimaging Toolbox

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          Abstract

          In the past years, mass univariate statistical analyses of neuroimaging data have been complemented by the use of multivariate pattern analyses, especially based on machine learning models. While these allow an increased sensitivity for the detection of spatially distributed effects compared to univariate techniques, they lack an established and accessible software framework. The goal of this work was to build a toolbox comprising all the necessary functionalities for multivariate analyses of neuroimaging data, based on machine learning models. The “Pattern Recognition for Neuroimaging Toolbox” (PRoNTo) is open-source, cross-platform, MATLAB-based and SPM compatible, therefore being suitable for both cognitive and clinical neuroscience research. In addition, it is designed to facilitate novel contributions from developers, aiming to improve the interaction between the neuroimaging and machine learning communities. Here, we introduce PRoNTo by presenting examples of possible research questions that can be addressed with the machine learning framework implemented in PRoNTo, and cannot be easily investigated with mass univariate statistical analysis.

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          Most cited references 41

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          Distributed and overlapping representations of faces and objects in ventral temporal cortex.

          The functional architecture of the object vision pathway in the human brain was investigated using functional magnetic resonance imaging to measure patterns of response in ventral temporal cortex while subjects viewed faces, cats, five categories of man-made objects, and nonsense pictures. A distinct pattern of response was found for each stimulus category. The distinctiveness of the response to a given category was not due simply to the regions that responded maximally to that category, because the category being viewed also could be identified on the basis of the pattern of response when those regions were excluded from the analysis. Patterns of response that discriminated among all categories were found even within cortical regions that responded maximally to only one category. These results indicate that the representations of faces and objects in ventral temporal cortex are widely distributed and overlapping.
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            Information-based functional brain mapping.

            The development of high-resolution neuroimaging and multielectrode electrophysiological recording provides neuroscientists with huge amounts of multivariate data. The complexity of the data creates a need for statistical summary, but the local averaging standardly applied to this end may obscure the effects of greatest neuroscientific interest. In neuroimaging, for example, brain mapping analysis has focused on the discovery of activation, i.e., of extended brain regions whose average activity changes across experimental conditions. Here we propose to ask a more general question of the data: Where in the brain does the activity pattern contain information about the experimental condition? To address this question, we propose scanning the imaged volume with a "searchlight," whose contents are analyzed multivariately at each location in the brain.
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              Automatic classification of patients with Alzheimer's disease from structural MRI: a comparison of ten methods using the ADNI database.

              Recently, several high dimensional classification methods have been proposed to automatically discriminate between patients with Alzheimer's disease (AD) or mild cognitive impairment (MCI) and elderly controls (CN) based on T1-weighted MRI. However, these methods were assessed on different populations, making it difficult to compare their performance. In this paper, we evaluated the performance of ten approaches (five voxel-based methods, three methods based on cortical thickness and two methods based on the hippocampus) using 509 subjects from the ADNI database. Three classification experiments were performed: CN vs AD, CN vs MCIc (MCI who had converted to AD within 18 months, MCI converters - MCIc) and MCIc vs MCInc (MCI who had not converted to AD within 18 months, MCI non-converters - MCInc). Data from 81 CN, 67 MCInc, 39 MCIc and 69 AD were used for training and hyperparameters optimization. The remaining independent samples of 81 CN, 67 MCInc, 37 MCIc and 68 AD were used to obtain an unbiased estimate of the performance of the methods. For AD vs CN, whole-brain methods (voxel-based or cortical thickness-based) achieved high accuracies (up to 81% sensitivity and 95% specificity). For the detection of prodromal AD (CN vs MCIc), the sensitivity was substantially lower. For the prediction of conversion, no classifier obtained significantly better results than chance. We also compared the results obtained using the DARTEL registration to that using SPM5 unified segmentation. DARTEL significantly improved six out of 20 classification experiments and led to lower results in only two cases. Overall, the use of feature selection did not improve the performance but substantially increased the computation times. Copyright © 2010 Elsevier Inc. All rights reserved.
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                Author and article information

                Contributors
                +44-20-76797214 , +44-20-73871397 , m.rosa@ucl.ac.uk
                Journal
                Neuroinformatics
                Neuroinformatics
                Neuroinformatics
                Springer US (Boston )
                1539-2791
                1559-0089
                16 February 2013
                16 February 2013
                July 2013
                : 11
                : 3
                : 319-337
                Affiliations
                [ ]Cyclotron Research Centre, University of Liège, Liège, Belgium
                [ ]Department of Computer Science, Centre for Computational Statistics and Machine Learning, University College London, Gower Street, WC1E 6BT London, UK
                [ ]Department of Neuroimaging, Centre for Neuroimaging Sciences, Institute of Psychiatry, King’s College London, London, UK
                [ ]Section on Functional Imaging Methods, Laboratory of Brain and Cognition, NIMH, NIH, Bethesda, USA
                [ ]Wellcome Trust Centre for NeuroImaging, University College London, London, UK
                [ ]Department of Electrical Engineering and Computer Science, University of Liège, Liège, Belgium
                [ ]Functional Imaging in Neuropsychiatric Disorders Lab, Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA
                [ ]Laboratory for Neurology & Imaging of Cognition, Departments of Neurosciences and Clinical Neurology, University of Geneva, Geneva, Switzerland
                [ ]Neuroimaging Laboratory, Department and Institute of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
                Article
                9178
                10.1007/s12021-013-9178-1
                3722452
                23417655
                f038a82e-8ab0-440f-94a5-3941c37b214e
                © The Author(s) 2013

                Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.

                Categories
                Original Article
                Custom metadata
                © Springer Science+Business Media New York 2013

                Neurosciences

                neuroimaging software, pattern recognition, machine learning, image analysis, mvpa

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