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      Scanning the horizon: towards transparent and reproducible neuroimaging research

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          Abstract

          Functional neuroimaging techniques have transformed our ability to probe the neurobiological basis of behaviour and are increasingly being applied by the wider neuroscience community. However, concerns have recently been raised that the conclusions that are drawn from some human neuroimaging studies are either spurious or

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          Using published data in Mendelian randomization: a blueprint for efficient identification of causal risk factors

          Stephen Burgess, Robert A H Scott, Nicholas J Timpson … (2015)
          Finding individual-level data for adequately-powered Mendelian randomization analyses may be problematic. As publicly-available summarized data on genetic associations with disease outcomes from large consortia are becoming more abundant, use of published data is an attractive analysis strategy for obtaining precise estimates of the causal effects of risk factors on outcomes. We detail the necessary steps for conducting Mendelian randomization investigations using published data, and present novel statistical methods for combining data on the associations of multiple (correlated or uncorrelated) genetic variants with the risk factor and outcome into a single causal effect estimate. A two-sample analysis strategy may be employed, in which evidence on the gene-risk factor and gene-outcome associations are taken from different data sources. These approaches allow the efficient identification of risk factors that are suitable targets for clinical intervention from published data, although the ability to assess the assumptions necessary for causal inference is diminished. Methods and guidance are illustrated using the example of the causal effect of serum calcium levels on fasting glucose concentrations. The estimated causal effect of a 1 standard deviation (0.13 mmol/L) increase in calcium levels on fasting glucose (mM) using a single lead variant from the CASR gene region is 0.044 (95 % credible interval −0.002, 0.100). In contrast, using our method to account for the correlation between variants, the corresponding estimate using 17 genetic variants is 0.022 (95 % credible interval 0.009, 0.035), a more clearly positive causal effect. Electronic supplementary material The online version of this article (doi:10.1007/s10654-015-0011-z) contains supplementary material, which is available to authorized users.
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            A unified statistical approach for determining significant signals in images of cerebral activation.

            K. J. Worsley, S Marrett, P Neelin … (1996)
            We present a unified statistical theory for assessing the significance of apparent signal observed in noisy difference images. The results are usable in a wide range of applications, including fMRI, but are discussed with particular reference to PET images which represent changes in cerebral blood flow elicited by a specific cognitive or sensorimotor task. Our main result is an estimate of the P-value for local maxima of Gaussian, t, chi(2) and F fields over search regions of any shape or size in any number of dimensions. This unifies the P-values for large search areas in 2-D (Friston et al. [1991]: J Cereb Blood Flow Metab 11:690-699) large search regions in 3-D (Worsley et al. [1992]: J Cereb Blood Flow Metab 12:900-918) and the usual uncorrected P-value at a single pixel or voxel. Copyright (c) 1996 Wiley-Liss, Inc.
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              Matching categorical object representations in inferior temporal cortex of man and monkey.

              Nikolaus Kriegeskorte, Marieke Mur, Douglas A Ruff … (2009)
              Inferior temporal (IT) object representations have been intensively studied in monkeys and humans, but representations of the same particular objects have never been compared between the species. Moreover, IT's role in categorization is not well understood. Here, we presented monkeys and humans with the same images of real-world objects and measured the IT response pattern elicited by each image. In order to relate the representations between the species and to computational models, we compare response-pattern dissimilarity matrices. IT response patterns form category clusters, which match between man and monkey. The clusters correspond to animate and inanimate objects; within the animate objects, faces and bodies form subclusters. Within each category, IT distinguishes individual exemplars, and the within-category exemplar similarities also match between the species. Our findings suggest that primate IT across species may host a common code, which combines a categorical and a continuous representation of objects.
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                Author and article information

                Journal
                Title: Nature Reviews Neuroscience
                Abbreviated Title: Nat Rev Neurosci
                Publisher: Springer Science and Business Media LLC
                ISSN (Print): 1471-003X
                ISSN (Electronic): 1471-0048
                Publication date Created: February 2017
                Publication date (Electronic): January 5 2017
                Publication date (Print): February 2017
                Volume: 18
                Issue: 2
                Pages: 115-126
                Article
                DOI: 10.1038/nrn.2016.167
                SO-VID: de11c557-8eba-4862-956e-558fb4188335
                Copyright © © 2017
                License:

                http://www.springer.com/tdm

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