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Kristanto D, Burkhardt M, Thiel C, Debener S, Gießing C, Hildebrandt A. The multiverse of data preprocessing and analysis in graph-based fMRI: A systematic literature review of analytical choices fed into a decision support tool for informed analysis. Neurosci Biobehav Rev 2024; 165:105846. [PMID: 39117132 DOI: 10.1016/j.neubiorev.2024.105846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/04/2024] [Accepted: 08/04/2024] [Indexed: 08/10/2024]
Abstract
The large number of different analytical choices used by researchers is partly responsible for the challenge of replication in neuroimaging studies. For an exhaustive robustness analysis, knowledge of the full space of analytical options is essential. We conducted a systematic literature review to identify the analytical decisions in functional neuroimaging data preprocessing and analysis in the emerging field of cognitive network neuroscience. We found 61 different steps, with 17 of them having debatable parameter choices. Scrubbing, global signal regression, and spatial smoothing are among the controversial steps. There is no standardized order in which different steps are applied, and the parameter settings within several steps vary widely across studies. By aggregating the pipelines across studies, we propose three taxonomic levels to categorize analytical choices: 1) inclusion or exclusion of specific steps, 2) parameter tuning within steps, and 3) distinct sequencing of steps. We have developed a decision support application with high educational value called METEOR to facilitate access to the data in order to design well-informed robustness (multiverse) analysis.
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Affiliation(s)
- Daniel Kristanto
- Department of Psychology, Carl von Ossietzky Universität Oldenburg, Oldenburg 26129, Germany.
| | - Micha Burkhardt
- Department of Psychology, Carl von Ossietzky Universität Oldenburg, Oldenburg 26129, Germany
| | - Christiane Thiel
- Department of Psychology, Carl von Ossietzky Universität Oldenburg, Oldenburg 26129, Germany; Research Center Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Germany; Cluster of Excellence "Hearing4All", Carl von Ossietzky Universität Oldenburg, Germany
| | - Stefan Debener
- Department of Psychology, Carl von Ossietzky Universität Oldenburg, Oldenburg 26129, Germany; Research Center Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Germany; Cluster of Excellence "Hearing4All", Carl von Ossietzky Universität Oldenburg, Germany
| | - Carsten Gießing
- Department of Psychology, Carl von Ossietzky Universität Oldenburg, Oldenburg 26129, Germany; Research Center Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Germany.
| | - Andrea Hildebrandt
- Department of Psychology, Carl von Ossietzky Universität Oldenburg, Oldenburg 26129, Germany; Research Center Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Germany; Cluster of Excellence "Hearing4All", Carl von Ossietzky Universität Oldenburg, Germany.
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Achard S, Coeurjolly JF, de Micheaux PL, Lbath H, Richiardi J. Inter-regional correlation estimators for functional magnetic resonance imaging. Neuroimage 2023; 282:120388. [PMID: 37805021 DOI: 10.1016/j.neuroimage.2023.120388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 09/05/2023] [Accepted: 09/22/2023] [Indexed: 10/09/2023] Open
Abstract
Functional magnetic resonance imaging (fMRI) functional connectivity between brain regions is often computed using parcellations defined by functional or structural atlases. Typically, some kind of voxel averaging is performed to obtain a single temporal correlation estimate per region pair. However, several estimators can be defined for this task, with various assumptions and degrees of robustness to local noise, global noise, and region size. In this paper, we systematically present and study the properties of 9 different functional connectivity estimators taking into account the spatial structure of fMRI data, based on a simple fMRI data spatial model. These include 3 existing estimators and 6 novel estimators. We demonstrate the empirical properties of the estimators using synthetic, animal, and human data, in terms of graph structure, repeatability and reproducibility, discriminability, dependence on region size, as well as local and global noise robustness. We prove analytically the link between regional intra-correlation and inter-region correlation, and show that the choice of estimator has a strong influence on inter-correlation values. Some estimators, including the commonly used correlation of averages (ca), are positively biased, and have more dependence to region size and intra-correlation than robust alternatives, resulting in spatially-dependent bias. We define the new local correlation of averages estimator with better theoretical guarantees, lower bias, significantly lower dependence on region size (Spearman correlation 0.40 vs 0.55, paired t-test T=27.2, p=1.1e-47), at negligible cost to discriminative power, compared to the ca estimator. The difference in connectivity pattern between the estimators is not distributed uniformly throughout the brain, but rather shows a clear ventral-dorsal gradient, suggesting that region size and intra-correlation plays an important role in shaping functional networks defined using the ca estimator, and leading to non-trivial differences in their connectivity structure. We provide an open source R package and equivalent Python implementation to facilitate the use of the new estimators, together with preprocessed rat time-series.
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Affiliation(s)
- Sophie Achard
- Univ. Grenoble Alpes, CNRS, Inria, Grenoble-INP, LJK, 38000 Grenoble, France.
| | | | - Pierre Lafaye de Micheaux
- AMIS, Université Paul Valéry Montpellier 3, France; PreMeDICaL - Precision Medicine by Data Integration and Causal Learning, Inria Sophia Antipolis, France; Desbrest Institute of Epidemiology and Public Health, Univ Montpellier, INSERM, Montpellier, France
| | - Hanâ Lbath
- Univ. Grenoble Alpes, CNRS, Inria, Grenoble-INP, LJK, 38000 Grenoble, France
| | - Jonas Richiardi
- Department of Radiology, Lausanne University Hospital and University of Lausanne, Switzerland
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Ogawa A, Osada T, Tanaka M, Suda A, Nakajima K, Oka S, Kamagata K, Aoki S, Oshima Y, Tanaka S, Hattori N, Konishi S. Hypothalamic interaction with reward-related regions during subjective evaluation of foods. Neuroimage 2022; 264:119744. [PMID: 36368500 DOI: 10.1016/j.neuroimage.2022.119744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/14/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022] Open
Abstract
The reward system implemented in the midbrain, ventral striatum, orbitofrontal cortex, and ventromedial prefrontal cortex evaluates and compares various types of rewards given to the organisms. It has been suggested that autonomic factors influence reward-related processing via the hypothalamus, but how the hypothalamus modulates the reward system remains elusive. In this functional magnetic resonance imaging study, the hypothalamus was parcellated into individual hypothalamic nuclei performing different autonomic functions using boundary mapping parcellation analyses. The effective interaction during subjective evaluation of foods in a reward task was then investigated between the human hypothalamic nuclei and the reward-related regions. We found significant brain activity decrease in the paraventricular nucleus (PVH) and lateral nucleus in the hypothalamus in food evaluation compared with monetary evaluation. A psychophysiological interaction analysis revealed dual interactions between the PVH and (1) midbrain region and (2) ventromedial prefrontal cortex, with the former correlated with the stronger tendency of participants toward food-seeking. A dynamic causal modeling analysis further revealed unidirectional interactions from the PVH to the midbrain and ventromedial prefrontal cortex. These results suggest that the PVH in the human hypothalamus interacts with the reward-related regions in the cerebral cortex via multiple pathways (i.e., the midbrain pathway and ventromedial prefrontal pathway) to evaluate rewards for subsequent decision-making.
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Affiliation(s)
- Akitoshi Ogawa
- Department of Neurophysiology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Takahiro Osada
- Department of Neurophysiology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Masaki Tanaka
- Department of Neurophysiology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Akimitsu Suda
- Department of Neurophysiology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; Department of Neurology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Koji Nakajima
- Department of Neurophysiology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; Department of Orthopaedic Surgery, The University of Tokyo School of Medicine, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satoshi Oka
- Department of Neurophysiology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Koji Kamagata
- Department of Radiology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Shigeki Aoki
- Department of Radiology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Yasushi Oshima
- Department of Orthopaedic Surgery, The University of Tokyo School of Medicine, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sakae Tanaka
- Department of Orthopaedic Surgery, The University of Tokyo School of Medicine, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Seiki Konishi
- Department of Neurophysiology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; Research Institute for Diseases of Old Age, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; Sportology Center, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; Advanced Research Institute for Health Science, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.
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Ogawa A. Time-varying measures of cerebral network centrality correlate with visual saliency during movie watching. Brain Behav 2021; 11:e2334. [PMID: 34435748 PMCID: PMC8442596 DOI: 10.1002/brb3.2334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/05/2021] [Accepted: 08/07/2021] [Indexed: 12/12/2022] Open
Abstract
The extensive development of graph-theoretic analysis for functional connectivity has revealed the multifaceted characteristics of brain networks. Network centralities identify the principal functional regions, individual differences, and hub structure in brain networks. Neuroimaging studies using movie-watching have investigated brain function under naturalistic stimuli. Visual saliency is one of the promising measures for revealing cognition and emotions driven by naturalistic stimuli. This study investigated whether the visual saliency in movies was associated with network centrality. The study examined eigenvector centrality (EC), which is a measure of a region's influence in the brain network, and the participation coefficient (PC), which reflects the hub structure in the brain, was used for comparison. Static and time-varying EC and PC were analyzed by a parcel-based technique. While EC was correlated with brain activity in parcels in the visual and auditory areas during movie-watching, it was only correlated with parcels in the visual areas in the retinotopy task. In addition, high PC was consistently observed in parcels in the putative hub both during the tasks and the resting-state condition. Time-varying EC in the parietal parcels and time-varying PC in the primary sensory parcels significantly correlated with visual saliency in the movies. These results suggest that time-varying centralities in brain networks are distinctively associated with perceptual processing and subsequent higher processing of visual saliency.
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Affiliation(s)
- Akitoshi Ogawa
- Faculty of Medicine, Juntendo University, Bunkyo-ku, Tokyo, Japan.,Brain Science Institute, Tamagawa University, Machida, Tokyo, Japan
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