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1. Predicting Parkinson's disease trajectory using clinical and functional MRI features: a reproduction and replication study

Author

Germani, Elodie, Baghwat, Nikhil, Dugré, Mathieu, Gau, Rémi, Montillo, Albert, Nguyen, Kevin, Sokolowski, Andrzej, Sharp, Madeleine, Poline, Jean-Baptiste, and Glatard, Tristan

Subjects
Quantitative Biology - Neurons and Cognition, Computer Science - Artificial Intelligence, Electrical Engineering and Systems Science - Image and Video Processing
Abstract

Parkinson's disease (PD) is a common neurodegenerative disorder with a poorly understood physiopathology and no established biomarkers for the diagnosis of early stages and for prediction of disease progression. Several neuroimaging biomarkers have been studied recently, but these are susceptible to several sources of variability. In this context, an evaluation of the robustness of such biomarkers is essential. This study is part of a larger project investigating the replicability of potential neuroimaging biomarkers of PD. Here, we attempt to reproduce (same data, same method) and replicate (different data or method) the models described in Nguyen et al., 2021 to predict individual's PD current state and progression using demographic, clinical and neuroimaging features (fALFF and ReHo extracted from resting-state fMRI). We use the Parkinson's Progression Markers Initiative dataset (PPMI, ppmi-info.org), as in Nguyen et al.,2021 and aim to reproduce the original cohort, imaging features and machine learning models as closely as possible using the information available in the paper and the code. We also investigated methodological variations in cohort selection, feature extraction pipelines and sets of input features. The success of the reproduction was assessed using different criteria. Notably, we obtained significantly better than chance performance using the analysis pipeline closest to that in the original study (R2 > 0), which is consistent with its findings. The challenges encountered while reproducing and replicating the original work are likely explained by the complexity of neuroimaging studies, in particular in clinical settings. We provide recommendations to further facilitate the reproducibility of such studies in the future.

Published
2024

2. The Past, Present, and Future of the Brain Imaging Data Structure (BIDS)

Author

Poldrack, Russell A., Markiewicz, Christopher J., Appelhoff, Stefan, Ashar, Yoni K., Auer, Tibor, Baillet, Sylvain, Bansal, Shashank, Beltrachini, Leandro, Benar, Christian G., Bertazzoli, Giacomo, Bhogawar, Suyash, Blair, Ross W., Bortoletto, Marta, Boudreau, Mathieu, Brooks, Teon L., Calhoun, Vince D., Castelli, Filippo Maria, Clement, Patricia, Cohen, Alexander L, Cohen-Adad, Julien, D'Ambrosio, Sasha, de Hollander, Gilles, de la iglesia-Vayá, María, de la Vega, Alejandro, Delorme, Arnaud, Devinsky, Orrin, Draschkow, Dejan, Duff, Eugene Paul, DuPre, Elizabeth, Earl, Eric, Esteban, Oscar, Feingold, Franklin W., Flandin, Guillaume, galassi, anthony, Gallitto, Giuseppe, Ganz, Melanie, Gau, Rémi, Gholam, James, Ghosh, Satrajit S., Giacomel, Alessio, Gillman, Ashley G, Gleeson, Padraig, Gramfort, Alexandre, Guay, Samuel, Guidali, Giacomo, Halchenko, Yaroslav O., Handwerker, Daniel A., Hardcastle, Nell, Herholz, Peer, Hermes, Dora, Honey, Christopher J., Innis, Robert B., Ioanas, Horea-Ioan, Jahn, Andrew, Karakuzu, Agah, Keator, David B., Kiar, Gregory, Kincses, Balint, Laird, Angela R., Lau, Jonathan C., Lazari, Alberto, Legarreta, Jon Haitz, Li, Adam, Li, Xiangrui, Love, Bradley C., Lu, Hanzhang, Maumet, Camille, Mazzamuto, Giacomo, Meisler, Steven L., Mikkelsen, Mark, Mutsaerts, Henk, Nichols, Thomas E., Nikolaidis, Aki, Nilsonne, Gustav, Niso, Guiomar, Norgaard, Martin, Okell, Thomas W, Oostenveld, Robert, Ort, Eduard, Park, Patrick J., Pawlik, Mateusz, Pernet, Cyril R., Pestilli, Franco, Petr, Jan, Phillips, Christophe, Poline, Jean-Baptiste, Pollonini, Luca, Raamana, Pradeep Reddy, Ritter, Petra, Rizzo, Gaia, Robbins, Kay A., Rockhill, Alexander P., Rogers, Christine, Rokem, Ariel, Rorden, Chris, Routier, Alexandre, Saborit-Torres, Jose Manuel, Salo, Taylor, Schirner, Michael, Smith, Robert E., Spisak, Tamas, Sprenger, Julia, Swann, Nicole C., Szinte, Martin, Takerkart, Sylvain, Thirion, Bertrand, Thomas, Adam G., Torabian, Sajjad, Varoquaux, Gael, Voytek, Bradley, Welzel, Julius, Wilson, Martin, Yarkoni, Tal, and Gorgolewski, Krzysztof J.

Subjects
Quantitative Biology - Other Quantitative Biology
Abstract

The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS.

Published
2023
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3. Variability in the analysis of a single neuroimaging dataset by many teams

Author

Botvinik-Nezer, Rotem, Holzmeister, Felix, Camerer, Colin F, Dreber, Anna, Huber, Juergen, Johannesson, Magnus, Kirchler, Michael, Iwanir, Roni, Mumford, Jeanette A, Adcock, R Alison, Avesani, Paolo, Baczkowski, Blazej M, Bajracharya, Aahana, Bakst, Leah, Ball, Sheryl, Barilari, Marco, Bault, Nadège, Beaton, Derek, Beitner, Julia, Benoit, Roland G, Berkers, Ruud MWJ, Bhanji, Jamil P, Biswal, Bharat B, Bobadilla-Suarez, Sebastian, Bortolini, Tiago, Bottenhorn, Katherine L, Bowring, Alexander, Braem, Senne, Brooks, Hayley R, Brudner, Emily G, Calderon, Cristian B, Camilleri, Julia A, Castrellon, Jaime J, Cecchetti, Luca, Cieslik, Edna C, Cole, Zachary J, Collignon, Olivier, Cox, Robert W, Cunningham, William A, Czoschke, Stefan, Dadi, Kamalaker, Davis, Charles P, Luca, Alberto De, Delgado, Mauricio R, Demetriou, Lysia, Dennison, Jeffrey B, Di, Xin, Dickie, Erin W, Dobryakova, Ekaterina, Donnat, Claire L, Dukart, Juergen, Duncan, Niall W, Durnez, Joke, Eed, Amr, Eickhoff, Simon B, Erhart, Andrew, Fontanesi, Laura, Fricke, G Matthew, Fu, Shiguang, Galván, Adriana, Gau, Remi, Genon, Sarah, Glatard, Tristan, Glerean, Enrico, Goeman, Jelle J, Golowin, Sergej AE, González-García, Carlos, Gorgolewski, Krzysztof J, Grady, Cheryl L, Green, Mikella A, Guassi Moreira, João F, Guest, Olivia, Hakimi, Shabnam, Hamilton, J Paul, Hancock, Roeland, Handjaras, Giacomo, Harry, Bronson B, Hawco, Colin, Herholz, Peer, Herman, Gabrielle, Heunis, Stephan, Hoffstaedter, Felix, Hogeveen, Jeremy, Holmes, Susan, Hu, Chuan-Peng, Huettel, Scott A, Hughes, Matthew E, Iacovella, Vittorio, Iordan, Alexandru D, Isager, Peder M, Isik, Ayse I, Jahn, Andrew, Johnson, Matthew R, Johnstone, Tom, Joseph, Michael JE, Juliano, Anthony C, Kable, Joseph W, Kassinopoulos, Michalis, Koba, Cemal, and Kong, Xiang-Zhen

Subjects
Generic health relevance, Brain, Data Analysis, Data Science, Datasets as Topic, Female, Functional Neuroimaging, Humans, Logistic Models, Magnetic Resonance Imaging, Male, Meta-Analysis as Topic, Models, Neurological, Reproducibility of Results, Research Personnel, Software, General Science & Technology
Abstract

Data analysis workflows in many scientific domains have become increasingly complex and flexible. Here we assess the effect of this flexibility on the results of functional magnetic resonance imaging by asking 70 independent teams to analyse the same dataset, testing the same 9 ex-ante hypotheses1. The flexibility of analytical approaches is exemplified by the fact that no two teams chose identical workflows to analyse the data. This flexibility resulted in sizeable variation in the results of hypothesis tests, even for teams whose statistical maps were highly correlated at intermediate stages of the analysis pipeline. Variation in reported results was related to several aspects of analysis methodology. Notably, a meta-analytical approach that aggregated information across teams yielded a significant consensus in activated regions. Furthermore, prediction markets of researchers in the field revealed an overestimation of the likelihood of significant findings, even by researchers with direct knowledge of the dataset2-5. Our findings show that analytical flexibility can have substantial effects on scientific conclusions, and identify factors that may be related to variability in the analysis of functional magnetic resonance imaging. The results emphasize the importance of validating and sharing complex analysis workflows, and demonstrate the need for performing and reporting multiple analyses of the same data. Potential approaches that could be used to mitigate issues related to analytical variability are discussed.

Published
2020

5. Open and reproducible neuroimaging: From study inception to publication

Author

Niso, Guiomar, Botvinik-Nezer, Rotem, Appelhoff, Stefan, De La Vega, Alejandro, Esteban, Oscar, Etzel, Joset A., Finc, Karolina, Ganz, Melanie, Gau, Rémi, Halchenko, Yaroslav O., Herholz, Peer, Karakuzu, Agah, Keator, David B., Markiewicz, Christopher J., Maumet, Camille, Pernet, Cyril R., Pestilli, Franco, Queder, Nazek, Schmitt, Tina, Sójka, Weronika, Wagner, Adina S., Whitaker, Kirstie J., and Rieger, Jochem W.

Published
2022
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6. PET-BIDS, an extension to the brain imaging data structure for positron emission tomography

Author

Norgaard, Martin, Matheson, Granville J., Hansen, Hanne D., Thomas, Adam, Searle, Graham, Rizzo, Gaia, Veronese, Mattia, Giacomel, Alessio, Yaqub, Maqsood, Tonietto, Matteo, Funck, Thomas, Gillman, Ashley, Boniface, Hugo, Routier, Alexandre, Dalenberg, Jelle R., Betthauser, Tobey, Feingold, Franklin, Markiewicz, Christopher J., Gorgolewski, Krzysztof J., Blair, Ross W., Appelhoff, Stefan, Gau, Remi, Salo, Taylor, Niso, Guiomar, Pernet, Cyril, Phillips, Christophe, Oostenveld, Robert, Gallezot, Jean-Dominique, Carson, Richard E., Knudsen, Gitte M., Innis, Robert B., and Ganz, Melanie

Published
2022
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7. ARTEM-IS for ERP: Agreed Reporting Template for EEG Methodology -International Standard for documenting studies on Event-Related Potentials

Author

Stekić, Katarina, Šoškić, Anđela, Vanja, Ković, Algermissen, Johannes, Fischer, Nastassja L., Ganis, Giorgio, Gau, Remi, Niso, Guiomar, Oostenveld, Robert, Pajić, Dejan, Paul, Mariella, Pavlov, Yuri, Yang, Yu-Fang, Styles, Suzy J, Stekić, Katarina, Šoškić, Anđela, Vanja, Ković, Algermissen, Johannes, Fischer, Nastassja L., Ganis, Giorgio, Gau, Remi, Niso, Guiomar, Oostenveld, Robert, Pajić, Dejan, Paul, Mariella, Pavlov, Yuri, Yang, Yu-Fang, and Styles, Suzy J

Abstract

Given that the choices made during recording, preprocessing and analysis of event-related potentials (ERP) data can affect study outcomes, it is critical that they are transparently reported to allow for reproducibility and replicability. Yet, systematic reviews of reporting practices in the field have shown that journal articles do not meet this goal and that guidelines for writing them better have not resulted in a sufficient improvement to reporting transparency.ARTEM-IS aims to address this issue by building dynamic, interactive web applications that support documenting information required by existing publication guidelines in the form of a standardised metadata template. Completing an ARTEM-IS form results in a human-reader-friendly PDF and a machine-readable JSON summary of methodological information, which allows for a level of reporting precision higher than what is typically found in journal articles. These can be used as supplements to a publication, as a memory aid when writing a paper, or as records that allow easier metadata extraction in comparison to verbal descriptions in papers.Here, we present the ARTEM-IS for ERP, which supports describing a typical ERP study, including most of its core methodological aspects (study description, experimental design, hardware, data acquisition, pre-processing, measurement, visualisation, additional comments). We discuss the current contents of the form, web application functionalities, current limitations, and potential directions for future developments. In addition, the process of building the form contents and the web application through a collaborative grassroots initiative is described. Finally, we argue that a wider adoption of ARTEM-IS can bring benefits to different stakeholders: researchers themselves or their collaborators, especially on large-scale projects, reviewers, readers of a paper, and the scientific community at large.

Published
2023

8. ARTEM-IS for ERP: Agreed Reporting Template for EEG Methodology - International Standard for documenting studies on Event-Related Potentials

Author

Šoškić, Anđela, primary, Kovic, Vanja, additional, Algermissen, Johannes, additional, Fischer, Nastassja Lopes, additional, Ganis, Giorgio, additional, Gau, Remi, additional, Niso, Guiomar, additional, Oostenveld, Robert, additional, Pajić, Dejan, additional, Paul, Mariella, additional, Pavlov, Yuri G., additional, Stekić, Katarina, additional, Yang, Yu-Fang, additional, and Styles, Suzy J, additional

Published
2023
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9. Brainhack: developing a culture of open, inclusive, community-driven neuroscience

Author

Gau, Remi, Noble, Stephanie, Heuer, Katja, Bottenhorn, Katherine, Bilgin, Isil, Yang, Yu-Fang, Huntenburg, Julia, Bayer, Johanna, Bethlehem, Richard, Rhoads, Shawn, Vogelbacher, Christoph, Borghesani, Valentina, Levitis, Elizabeth, Wang, Hao-Ting, Van Den Bossche, Sofie, Kobeleva, Xenia, Legarreta Gorroño, Jon Haitz, Guay, Samuel, ATAY, Melvin, Varoquaux, Gael, Huijser, Dorien, Sandström, Malin, Herholz, Peer, Nastase, Samuel, Badhwar, AmanPreet, Dumas, Guillaume, Schwab, Simon, Moia, Stefano, Dayan, Michael, Bassil, Yasmine, Brooks, Paula, Mancini, Matteo, Shine, James, O'Connor, David, Xie, Xihe, Poggiali, Davide, Friedrich, Patrick, Heinsfeld, Anibal, Riedl, Lydia, Toro, Roberto, Caballero-Gaudes, César, Eklund, Anders, Garner, Kelly, Nolan, Christopher, Demeter, Damion, Barrios, Fernando, Merchant, Junaid, McDevitt, Elizabeth, Oostenveld, Robert, Craddock, Cameron, Rokem, Ariel, Doyle, Andrew, Esper, Nathalia, Ghosh, Satrajit, Langs, Georg, Nikolaidis, Aki, Stanley, Olivia, Uruñuela, Eneko, Vohryzek, Jakub, and community, Brainhack

Subjects
neuroscience, inclusivity, training, hackathon, open science, best practices, Brainhack, reproducibility, collaboration, community building
Abstract

Brainhack is an innovative meeting format that promotes scientific collaboration and education in an open and inclusive environment. Departing from the formats of typical scientific workshops, these events are based on grassroots projects and training, and foster open and reproducible scientific practices. We describe here the multifaceted, lasting benefits of Brainhacks for individual participants, particularly early career researchers. We further highlight the unique contributions that Brainhacks can make to the research community, contributing to scientific progress by complementing opportunities available in conventional formats.

Published
2022
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10. Lab manuals for efficient and high quality science in a happy and safe work environment

Author

Kovacs, Marton, Kouros, Chrystyna, Gokce, Ahu, Algermissen, Johannes, Jaquiery, Matt, Yeung, Siu Kit, Gau, Remi, Arriaga, Patricia, Grassi, Massimo, and Aczel, Balazs

Subjects
MetaArXiv|Social and Behavioral Sciences, bepress|Social and Behavioral Sciences, bepress|Medicine and Health Sciences, MetaArXiv|Medicine and Health Sciences
Abstract

The culture and norms of research laboratories can greatly influence the quality of scientific outputs produced by the lab and the well-being of its members. In most labs, the culture that governs how individual researchers behave in their work is often implicit and situational. In contrast, some labs develop their own lab manual, a written document that outlines their standard functioning. Such a lab manual can ensure that lab members have a shared and mutual understanding of who they are and how they do things. We argue that every lab could benefit from a lab manual because it facilitates efficient collaboration, reduces potential research mistakes, and aids the integration of new good research practices.Developing a lab manual without a doubt requires extra effort. To decrease researchers’ burden of creating their own lab manual, we provide a lab manual template that outlines the different topics that could be included in a manual. Moreover, we introduce an easy-to-use web app, blueprint, that further simplifies the process of creating a lab manual using our template. The present paper aims to serve as a guide for those who would like to partake in this endeavor.

Published
2022

15. NARPS - CPPL

Author

Gau, Remi and Barilari, Marco

Abstract

Participation of the CPPL to the NARPS project (https://www.narps.info/)

Published
2022
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16. ARTEM-IS Web App OHBM Brainhack 2021

Author

Styles, Suzy, Šoškić, Anđela, Kovic, Vanja, Ke, Han, Gau, Remi, Pavlov, Yuri, Woon, Fei Ting, Yang, Yu-Fang, Fischer, Nastassja, Niso, Guiomar, Sareen, Ekansh, Algermissen, Johannes, Sundaray, Shamala, Tan, Jasmine, Yap, De Fu, Ganis, Giorgio, and Shaw, Alec

Published
2022
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20. EEG ERP Preregistration Template

Author

Govaart, Gisela Hanna, primary, Schettino, Antonio, additional, Helbling, Saskia, additional, Mehler, David Marc Anton, additional, Ngiam, William Xiang Quan, additional, Moreau, David, additional, Chiossi, Francesco, additional, Zanesco, Anthony Paul, additional, Yang, Yu-Fang, additional, Gau, Remi, additional, Bartlett, James Edward, additional, García Alanis, José C., additional, Gutsell, Jennifer Nadine, additional, Çetinçelik, Melis, additional, Pavlov, Yuri G., additional, Šoškić, Anđela, additional, Ehinger, Benedikt Valerian, additional, Mouseli, Pedram, additional, Algermissen, Johannes, additional, Topor, Marta, additional, Pérez-Navarro, Jose, additional, Häberle, Greta, additional, Schreiner, Melanie Steffi, additional, Rothmaler, Katrin, additional, Niso, Guiomar, additional, and Paul, Mariella, additional

Published
2022
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22. Auditory and visual motion processing in hMT+/V5: preliminary results at 7T fMRI.

Author

UCL - SSH/IPSY - Psychological Sciences Research Institute, UCL - SSS/IONS/COSY - Systems & cognitive Neuroscience, The Introduction Sense Innovation and Research Center - School of Health Sciences, HES-SO, Barilari, Marco, Gau, Remi, Collignon, Olivier, UCL - SSH/IPSY - Psychological Sciences Research Institute, UCL - SSS/IONS/COSY - Systems & cognitive Neuroscience, The Introduction Sense Innovation and Research Center - School of Health Sciences, HES-SO, Barilari, Marco, Gau, Remi, and Collignon, Olivier

Abstract

The ability of the brain to integrate motion information originating from separate sensory modalities is fundamental to efficiently interact with our dynamic environment. The human occipito-temporal region hMT+/V5 is known to be highly specialized to process visual motion directions. In addition to its role in processing the dominant visual information, it was recently suggested that this region may also engage in crossmodal motion processing from the auditory modality. How multisensory information is represented in this region remains however poorly understood. To further investigate the multisensory nature of hMT+/V5, we characterized single-subject activity with ultra-high field (UHF) fMRI when participants processed horizontal and vertical motion stimuli delivered through vision, audition, or a combination of both modalities simultaneously. Our preliminary results confirmed that in addition to a robust selectivity for visual motion, portion of hMT+/V5 selectively responds to moving sounds. We are now further characterizing the brain activity in the cortical depths using UHF fMRI combined with vascular space occupancy (VASO) recording at high spatial resolution (.75mm isotropic). We hypothesize that hMT+/V5 might encode auditory and visual motion information in separate cortical layers, reflecting the feed-forward versus feed-back nature of how sensory information flows into those regions. This project will shed new lights on how crossmodal information is represented across the depth of the cortical layers of motion selective human brain areas.

Published
2022

23. Characterizing auditory and visual motion processing and integration using submillimeter 7T fMRI: preliminary data

Author

UCL - SSH/IPSY - Psychological Sciences Research Institute, UCL - SSS/IONS/COSY - Systems & cognitive Neuroscience, University Of Liege - GIGA Cyclotron Research Centre in vivo imaging, The Sense Innovation and Research Center, - School of Health Sciences, Barilari, Marco, Gau, Remi, Battal, Ceren, Sherif, Syia, UCL - SSH/IPSY - Psychological Sciences Research Institute, UCL - SSS/IONS/COSY - Systems & cognitive Neuroscience, University Of Liege - GIGA Cyclotron Research Centre in vivo imaging, The Sense Innovation and Research Center, - School of Health Sciences, Barilari, Marco, Gau, Remi, Battal, Ceren, and Sherif, Syia

Abstract

The ability of the brain to integrate motion information originating from separate sensory modalities is fundamental to efficiently interact with our dynamic environment. The human occipito-temporal visual region hMT+/V5 and the auditory area Planum Temporale (PT) are known to be highly specialized to process visual and auditory motion directions, respectively. In addition to their role in processing the dominant sensory information, it was recently suggested that these regions may also engage in crossmodal motion processing. How multisensory information is represented in these regions remain however poorly understood. To further investigate the multisensory nature of hMT+/V5 and PT, we characterized single-subject activity with ultra-high field (UHF) fMRI (7T) when participants processed horizontal and vertical motion stimuli delivered through vision, audition, or a combination of both modalities simultaneously. Our preliminary results confirmed that in addition to a robust selectivity for visual motion, portion of hMT+/V5 selectively responds to moving sounds and a portion of PT responds to moving visual stimuli. We are now further characterizing the brain activity in the cortical depths using UHF fMRI combined with vascular space occupancy (VASO) recording at high spatial resolution (.75mm isotropic). We hypothesize that hMT+/V5 and PT might encode auditory and visual motion information in separate cortical layers, reflecting the feed-forward versus feed-back nature of how sensory information flows into those regions. This project will shed new lights on how crossmodal information is represented across the depth of the cortical layers of motion selective human brain areas.

Published
2022

24. Open and reproducible neuroimaging: from study inception to publication

Author

Niso, Guiomar, primary, Botvinik-Nezer, Rotem, additional, Appelhoff, Stefan, additional, De La Vega, Alejandro, additional, Esteban, Oscar, additional, Etzel, Joset A., additional, Finc, Karolina, additional, Ganz, Melanie, additional, Gau, Remi, additional, Halchenko, Yaroslav O, additional, Herholz, Peer, additional, Karakuzu, Agah, additional, Keator, David, additional, MAUMET, Camille, additional, Markiewicz, Christopher Johnson, additional, Pernet, Cyril R, additional, Pestilli, Franco, additional, Queder, Nazek, additional, Schmitt, Tina, additional, Sójka, Weronika, additional, Wagner, Adina Svenja, additional, Whitaker, Kirstie Jane, additional, and Rieger, Jochem, additional

Published
2022
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25. Auditory and visual motion processing in hMT+/V5: preliminary results at 7T fMRI

Author

Barilari, Marco, Gau, Remi, Collignon, Olivier, UCL - SSH/IPSY - Psychological Sciences Research Institute, UCL - SSS/IONS/COSY - Systems & cognitive Neuroscience, and The Introduction Sense Innovation and Research Center - School of Health Sciences, HES-SO

Subjects
multisensory, 7T, fMRI, vado, Neuroimaging, layers, high-field mri
Abstract

The ability of the brain to integrate motion information originating from separate sensory modalities is fundamental to efficiently interact with our dynamic environment. The human occipito-temporal region hMT+/V5 is known to be highly specialized to process visual motion directions. In addition to its role in processing the dominant visual information, it was recently suggested that this region may also engage in crossmodal motion processing from the auditory modality. How multisensory information is represented in this region remains however poorly understood. To further investigate the multisensory nature of hMT+/V5, we characterized single-subject activity with ultra-high field (UHF) fMRI when participants processed horizontal and vertical motion stimuli delivered through vision, audition, or a combination of both modalities simultaneously. Our preliminary results confirmed that in addition to a robust selectivity for visual motion, portion of hMT+/V5 selectively responds to moving sounds. We are now further characterizing the brain activity in the cortical depths using UHF fMRI combined with vascular space occupancy (VASO) recording at high spatial resolution (.75mm isotropic). We hypothesize that hMT+/V5 might encode auditory and visual motion information in separate cortical layers, reflecting the feed-forward versus feed-back nature of how sensory information flows into those regions. This project will shed new lights on how crossmodal information is represented across the depth of the cortical layers of motion selective human brain areas.

Published
2022

26. Characterizing auditory and visual motion processing and integration using submillimeter 7T fMRI: preliminary data

Author

Barilari, Marco, Gau, Remi, Battal, Ceren, Sherif, Syia, Collignon, Olivier, UCL - SSH/IPSY - Psychological Sciences Research Institute, UCL - SSS/IONS/COSY - Systems & cognitive Neuroscience, University Of Liege - GIGA Cyclotron Research Centre in vivo imaging, and The Sense Innovation and Research Center, - School of Health Sciences

Subjects
multisensory, 7T, fMRI, Neuroimaging, layers, vaso, high-field mri
Abstract

The ability of the brain to integrate motion information originating from separate sensory modalities is fundamental to efficiently interact with our dynamic environment. The human occipito-temporal visual region hMT+/V5 and the auditory area Planum Temporale (PT) are known to be highly specialized to process visual and auditory motion directions, respectively. In addition to their role in processing the dominant sensory information, it was recently suggested that these regions may also engage in crossmodal motion processing. How multisensory information is represented in these regions remain however poorly understood. To further investigate the multisensory nature of hMT+/V5 and PT, we characterized single-subject activity with ultra-high field (UHF) fMRI (7T) when participants processed horizontal and vertical motion stimuli delivered through vision, audition, or a combination of both modalities simultaneously. Our preliminary results confirmed that in addition to a robust selectivity for visual motion, portion of hMT+/V5 selectively responds to moving sounds and a portion of PT responds to moving visual stimuli. We are now further characterizing the brain activity in the cortical depths using UHF fMRI combined with vascular space occupancy (VASO) recording at high spatial resolution (.75mm isotropic). We hypothesize that hMT+/V5 and PT might encode auditory and visual motion information in separate cortical layers, reflecting the feed-forward versus feed-back nature of how sensory information flows into those regions. This project will shed new lights on how crossmodal information is represented across the depth of the cortical layers of motion selective human brain areas.

Published
2022

29. PET-BIDS, an extension to the brain imaging data structure for positron emission tomography

Author

Norgaard, Martin, primary, Matheson, Granville J., additional, Hansen, Hanne D., additional, Thomas, Adam, additional, Searle, Graham, additional, Rizzo, Gaia, additional, Veronese, Mattia, additional, Giacomel, Alessio, additional, Yaqub, Maqsood, additional, Tonietto, Matteo, additional, Funck, Thomas, additional, Gillman, Ashley, additional, Boniface, Hugo, additional, Routier, Alexandre, additional, Dalenberg, Jelle R., additional, Betthauser, Tobey, additional, Feingold, Franklin, additional, Markiewicz, Christopher J., additional, Gorgolewski, Krzysztof J., additional, Blair, Ross W., additional, Appelhoff, Stefan, additional, Gau, Remi, additional, Salo, Taylor, additional, Niso, Guiomar, additional, Pernet, Cyril, additional, Phillips, Christophe, additional, Oostenveld, Robert, additional, Gallezot, Jean-Dominique, additional, Carson, Richard E., additional, Knudsen, Gitte M., additional, Innis, Robert B., additional, and Ganz, Melanie, additional

Published
2021
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30. PET-BIDS, an extension to the brain imaging data structure for positron emission tomography

Author

Nørgaard, Martin, Matheson, Granville J, Hansen, Hanne D, Thomas, Adam, Searle, Graham, Rizzo, Gaia, Veronese, Mattia, Giacomel, Alessio, Yaqub, Maqsood, Tonietto, Matteo, Funck, Thomas, Gillman, Ashley, Boniface, Hugo, Routier, Alexandre, Dalenberg, Jelle R, Betthauser, Tobey, Feingold, Franklin, Markiewicz, Christopher J, Gorgolewski, Krzysztof J, Blair, Ross W, Appelhoff, Stefan, Gau, Remi, Salo, Taylor, Niso, Guiomar, Pernet, Cyril, Phillips, Christophe, Oostenveld, Robert, Gallezot, Jean-Dominique, Carson, Richard E, Knudsen, Gitte M, Innis, Robert B, and Ganz, Melanie

Subjects
ComputingMilieux_COMPUTERSANDSOCIETY, heterocyclic compounds, biological phenomena, cell phenomena, and immunity, urologic and male genital diseases, neoplasms, GeneralLiterature_MISCELLANEOUS, digestive system diseases
Abstract

The Brain Imaging Data Structure (BIDS) is a standard for organizing and describing neuroimaging datasets. It serves not only to facilitate the process of data sharing and aggregation, but also to simplify the application and development of new methods and software for working with neuroimaging data. Here, we present an extension of BIDS to include positron emission tomography (PET) data (PET-BIDS). We describe the PET-BIDS standard in detail and share several open-access datasets curated following PET-BIDS. Additionally, we highlight several tools which are already available for converting, validating and analyzing PET-BIDS datasets.Competing Interest StatementThe authors have declared no competing interest.

Published
2021

31. Characterizing auditory and visual motion processing and integration in hMT+/V5 with ultra-high-field fMRI (7T): very preliminary results

Author

Barilari, Marco, Gau, Remi, Huber, Renzo, Collignon, Olivier, UCL - SSH/IPSY - Psychological Sciences Research Institute, and UCL - SSS/IONS/COSY - Systems & cognitive Neuroscience

Subjects
multisensory, 7T, fMRI, Neuroimaging, layers, vaso, high-field mri
Abstract

The ability of the brain to integrate motion information originating from separate sensory modalities is fundamental to efficiently interact with our dynamic environment. The human occipito-temporal region hMT+/V5 is known to be highly specialized to process visual motion directions. In addition to its role in processing the dominant visual information, it was recently suggested that this region may also engage in crossmodal motion processing from the auditory modality. How multisensory information is represented in this region remains however poorly understood. To further investigate the multisensory nature of hMT+/V5, we characterized single- subject activity with ultra-high field (UHF) fMRI using a visual motion stimulation together with highly ecological directional motion sounds recorded with in-ear microphones from horizontal and vertical speaker arrays. Moreover, we outlined the crossmodal input profile in functionally mapped subregions MT and MST. Our preliminary results confirmed that in addition to a robust selectivity for visual motion, portion of hMT+/V5 selectively responds to moving sounds. We are now further characterizing the brain activity in the cortical depths using UHF fMRI combined with vascular space occupancy (VASO) recording at high spatial resolution (.75mm isotropic). We hypothesize that hMT+/V5 might encode auditory and visual motion information in separate cortical layers, reflecting the feed-forward versus feed-back nature of how sensory information flows into those regions. This project will shed new lights on how crossmodal information is represented across the depth of the cortical layers of motion selective human brain areas.

Published
2021

32. Brainhack: Developing a culture of open, inclusive, community-driven neuroscience.

Author

UCL - SSH/IPSY - Psychological Sciences Research Institute, Gau, Remi, Noble, Stephanie, Heuer, Katja, Bottenhorn, Katherine L, Bilgin, Isil P, Yang, Yu-Fang, Huntenburg, Julia M, Bayer, Johanna M M, Bethlehem, Richard A I, Rhoads, Shawn A, Vogelbacher, Christoph, Borghesani, Valentina, Levitis, Elizabeth, Wang, Hao-Ting, Van Den Bossche, Sofie, Kobeleva, Xenia, Legarreta, Jon Haitz, Guay, Samuel, Atay, Selim Melvin, Varoquaux, Gael P, Huijser, Dorien C, Sandström, Malin S, Herholz, Peer, Nastase, Samuel A, Badhwar, AmanPreet, Dumas, Guillaume, Schwab, Simon, Moia, Stefano, Dayan, Michael, Bassil, Yasmine, Brooks, Paula P, Mancini, Matteo, Shine, James M, O'Connor, David, Xie, Xihe, Poggiali, Davide, Friedrich, Patrick, Heinsfeld, Anibal S, Riedl, Lydia, Toro, Roberto, Caballero-Gaudes, César, Eklund, Anders, Garner, Kelly G, Nolan, Christopher R, Demeter, Damion V, Barrios, Fernando A, Merchant, Junaid S, McDevitt, Elizabeth A, Oostenveld, Robert, Craddock, R Cameron, Rokem, Ariel, Doyle, Andrew, Ghosh, Satrajit S, Nikolaidis, Aki, Stanley, Olivia W, Uruñuela, Eneko, Brainhack Community, UCL - SSH/IPSY - Psychological Sciences Research Institute, Gau, Remi, Noble, Stephanie, Heuer, Katja, Bottenhorn, Katherine L, Bilgin, Isil P, Yang, Yu-Fang, Huntenburg, Julia M, Bayer, Johanna M M, Bethlehem, Richard A I, Rhoads, Shawn A, Vogelbacher, Christoph, Borghesani, Valentina, Levitis, Elizabeth, Wang, Hao-Ting, Van Den Bossche, Sofie, Kobeleva, Xenia, Legarreta, Jon Haitz, Guay, Samuel, Atay, Selim Melvin, Varoquaux, Gael P, Huijser, Dorien C, Sandström, Malin S, Herholz, Peer, Nastase, Samuel A, Badhwar, AmanPreet, Dumas, Guillaume, Schwab, Simon, Moia, Stefano, Dayan, Michael, Bassil, Yasmine, Brooks, Paula P, Mancini, Matteo, Shine, James M, O'Connor, David, Xie, Xihe, Poggiali, Davide, Friedrich, Patrick, Heinsfeld, Anibal S, Riedl, Lydia, Toro, Roberto, Caballero-Gaudes, César, Eklund, Anders, Garner, Kelly G, Nolan, Christopher R, Demeter, Damion V, Barrios, Fernando A, Merchant, Junaid S, McDevitt, Elizabeth A, Oostenveld, Robert, Craddock, R Cameron, Rokem, Ariel, Doyle, Andrew, Ghosh, Satrajit S, Nikolaidis, Aki, Stanley, Olivia W, Uruñuela, Eneko, and Brainhack Community

Abstract

Brainhack is an innovative meeting format that promotes scientific collaboration and education in an open, inclusive environment. This NeuroView describes the myriad benefits for participants and the research community and how Brainhacks complement conventional formats to augment scientific progress.

Published
2021

33. Characterizing auditory and visual motion processing and integration in hMT+/V5 with ultra-high-field fMRI (7T): very preliminary results.

Author

UCL - SSH/IPSY - Psychological Sciences Research Institute, UCL - SSS/IONS/COSY - Systems & cognitive Neuroscience, Barilari, Marco, Gau, Remi, Huber, Renzo, Collignon, Olivier, UCL - SSH/IPSY - Psychological Sciences Research Institute, UCL - SSS/IONS/COSY - Systems & cognitive Neuroscience, Barilari, Marco, Gau, Remi, Huber, Renzo, and Collignon, Olivier

Abstract

The ability of the brain to integrate motion information originating from separate sensory modalities is fundamental to efficiently interact with our dynamic environment. The human occipito-temporal region hMT+/V5 is known to be highly specialized to process visual motion directions. In addition to its role in processing the dominant visual information, it was recently suggested that this region may also engage in crossmodal motion processing from the auditory modality. How multisensory information is represented in this region remains however poorly understood. To further investigate the multisensory nature of hMT+/V5, we characterized single- subject activity with ultra-high field (UHF) fMRI using a visual motion stimulation together with highly ecological directional motion sounds recorded with in-ear microphones from horizontal and vertical speaker arrays. Moreover, we outlined the crossmodal input profile in functionally mapped subregions MT and MST. Our preliminary results confirmed that in addition to a robust selectivity for visual motion, portion of hMT+/V5 selectively responds to moving sounds. We are now further characterizing the brain activity in the cortical depths using UHF fMRI combined with vascular space occupancy (VASO) recording at high spatial resolution (.75mm isotropic). We hypothesize that hMT+/V5 might encode auditory and visual motion information in separate cortical layers, reflecting the feed-forward versus feed-back nature of how sensory information flows into those regions. This project will shed new lights on how crossmodal information is represented across the depth of the cortical layers of motion selective human brain areas.

Published
2021

34. Resolving multisensory and attentional influences across cortical depth in sensory cortices.

Author

UCL - SSH/IPSY - Psychological Sciences Research Institute, Gau, Remi, Bazin, Pierre-Louis, Trampel, Robert, Turner, Robert, Noppeney, Uta, UCL - SSH/IPSY - Psychological Sciences Research Institute, Gau, Remi, Bazin, Pierre-Louis, Trampel, Robert, Turner, Robert, and Noppeney, Uta

Abstract

In our environment, our senses are bombarded with a myriad of signals, only a subset of which is relevant for our goals. Using sub-millimeter-resolution fMRI at 7T, we resolved BOLD-response and activation patterns across cortical depth in early sensory cortices to auditory, visual and audiovisual stimuli under auditory or visual attention. In visual cortices, auditory stimulation induced widespread inhibition irrespective of attention, whereas auditory relative to visual attention suppressed mainly central visual field representations. In auditory cortices, visual stimulation suppressed activations, but amplified responses to concurrent auditory stimuli, in a patchy topography. Critically, multisensory interactions in auditory cortices were stronger in deeper laminae, while attentional influences were greatest at the surface. These distinct depth-dependent profiles suggest that multisensory and attentional mechanisms regulate sensory processing via partly distinct circuitries. Our findings are crucial for understanding how the brain regulates information flow across senses to interact with our complex multisensory world.

Published
2020

38. Variability in the analysis of a single neuroimaging dataset by many teams

Author

Botvinik-Nezer, Rotem, primary, Holzmeister, Felix, additional, Camerer, Colin F., additional, Dreber, Anna, additional, Huber, Juergen, additional, Johannesson, Magnus, additional, Kirchler, Michael, additional, Iwanir, Roni, additional, Mumford, Jeanette A., additional, Adcock, Alison, additional, Avesani, Paolo, additional, Baczkowski, Blazej, additional, Bajracharya, Aahana, additional, Bakst, Leah, additional, Ball, Sheryl, additional, Barilari, Marco, additional, Bault, Nadège, additional, Beaton, Derek, additional, Beitner, Julia, additional, Benoit, Roland, additional, Berkers, Ruud, additional, Bhanji, Jamil, additional, Biswal, Bharat, additional, Bobadilla-Suarez, Sebastian, additional, Bortolini, Tiago, additional, Bottenhorn, Katherine, additional, Bowring, Alexander, additional, Braem, Senne, additional, Brooks, Hayley, additional, Brudner, Emily, additional, Calderon, Cristian, additional, Camilleri, Julia, additional, Castrellon, Jaime, additional, Cecchetti, Luca, additional, Cieslik, Edna, additional, Cole, Zachary, additional, Collignon, Olivier, additional, Cox, Robert, additional, Cunningham, William, additional, Czoschke, Stefan, additional, Dadi, Kamalaker, additional, Davis, Charles, additional, De Luca, Alberto, additional, Delgado, Mauricio, additional, Demetriou, Lysia, additional, Dennison, Jeffrey, additional, Di, Xin, additional, Dickie, Erin, additional, Dobryakova, Ekaterina, additional, Donnat, Claire, additional, Dukart, Juergen, additional, Duncan, Niall W., additional, Durnez, Joke, additional, Eed, Amr, additional, Eickhoff, Simon, additional, Erhart, Andrew, additional, Fontanesi, Laura, additional, Fricke, G. Matthew, additional, Galvan, Adriana, additional, Gau, Remi, additional, Genon, Sarah, additional, Glatard, Tristan, additional, Glerean, Enrico, additional, Goeman, Jelle, additional, Golowin, Sergej, additional, González-García, Carlos, additional, Gorgolewski, Krzysztof, additional, Grady, Cheryl, additional, Green, Mikella, additional, Guassi Moreira, João, additional, Guest, Olivia, additional, Hakimi, Shabnam, additional, Hamilton, J. Paul, additional, Hancock, Roeland, additional, Handjaras, Giacomo, additional, Harry, Bronson, additional, Hawco, Colin, additional, Herholz, Peer, additional, Herman, Gabrielle, additional, Heunis, Stephan, additional, Hoffstaedter, Felix, additional, Hogeveen, Jeremy, additional, Holmes, Susan, additional, Hu, Chuan-Peng, additional, Huettel, Scott, additional, Hughes, Matthew, additional, Iacovella, Vittorio, additional, Iordan, Alexandru, additional, Isager, Peder, additional, Isik, Ayse Ilkay, additional, Jahn, Andrew, additional, Johnson, Matthew, additional, Johnstone, Tom, additional, Joseph, Michael, additional, Juliano, Anthony, additional, Kable, Joseph, additional, Kassinopoulos, Michalis, additional, Koba, Cemal, additional, Kong, Xiang-Zhen, additional, Koscik, Timothy, additional, Kucukboyaci, Nuri Erkut, additional, Kuhl, Brice, additional, Kupek, Sebastian, additional, Laird, Angela, additional, Lamm, Claus, additional, Langner, Robert, additional, Lauharatanahirun, Nina, additional, Lee, Hongmi, additional, Lee, Sangil, additional, Leemans, Alexander, additional, Leo, Andrea, additional, Lesage, Elise, additional, Li, Flora, additional, Li, Monica, additional, Lim, Phui Cheng, additional, Lintz, Evan, additional, Liphardt, Schuyler, additional, Losecaat Vermeer, Annabel, additional, Love, Bradley, additional, Mack, Michael, additional, Malpica, Norberto, additional, Marins, Theo, additional, Maumet, Camille, additional, McDonald, Kelsey, additional, McGuire, Joseph, additional, Melero, Helena, additional, Méndez Leal, Adriana, additional, Meyer, Benjamin, additional, Meyer, Kristin, additional, Mihai, Paul, additional, Mitsis, Georgios, additional, Moll, Jorge, additional, Nielson, Dylan, additional, Nilsonne, Gustav, additional, Notter, Michael, additional, Olivetti, Emanuele, additional, Onicas, Adrian, additional, Papale, Paolo, additional, Patil, Kaustubh, additional, Peelle, Jonathan E., additional, Pérez, Alexandre, additional, Pischedda, Doris, additional, Poline, Jean-Baptiste, additional, Prystauka, Yanina, additional, Ray, Shruti, additional, Reuter-Lorenz, Patricia, additional, Reynolds, Richard, additional, Ricciardi, Emiliano, additional, Rieck, Jenny, additional, Rodriguez-Thompson, Anais, additional, Romyn, Anthony, additional, Salo, Taylor, additional, Samanez-Larkin, Gregory, additional, Sanz-Morales, Emilio, additional, Schlichting, Margaret, additional, Schultz, Douglas, additional, Shen, Qiang, additional, Sheridan, Margaret, additional, Shiguang, Fu, additional, Silvers, Jennifer, additional, Skagerlund, Kenny, additional, Smith, Alec, additional, Smith, David, additional, Sokol-Hessner, Peter, additional, Steinkamp, Simon, additional, Tashjian, Sarah, additional, Thirion, Bertrand, additional, Thorp, John, additional, Tinghög, Gustav, additional, Tisdall, Loreen, additional, Tompson, Steven, additional, Toro-Serey, Claudio, additional, Torre, Juan, additional, Tozzi, Leonardo, additional, Truong, Vuong, additional, Turella, Luca, additional, van’t Veer, Anna E., additional, Verguts, Tom, additional, Vettel, Jean, additional, Vijayarajah, Sagana, additional, Vo, Khoi, additional, Wall, Matthew, additional, Weeda, Wouter D., additional, Weis, Susanne, additional, White, David, additional, Wisniewski, David, additional, Xifra-Porxas, Alba, additional, Yearling, Emily, additional, Yoon, Sangsuk, additional, Yuan, Rui, additional, Yuen, Kenneth, additional, Zhang, Lei, additional, Zhang, Xu, additional, Zosky, Joshua, additional, Nichols, Thomas E., additional, Poldrack, Russell A., additional, and Schonberg, Tom, additional

Published
2019
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39. COBIDAS checklist

Author

Wiebels, Kristina, Tepper, Angie, Simon, Jeremy, Van Praag, Cassandra Gould, Bartlett, James E, Hortensius, Ruud, Van Mourik, Tim, Ruotsalainen, Ilona, Gau, Remi, Scarpazza, Cristina, Sjoerds, Zsuzsika, Moreau, David, Klapwijk, Eduard, and Adolfi, Federico G

Subjects
MEG, PET, fMRI, EEG, checklist
Abstract

Using a checklist to help with more thorough and transparent methods and result reporting in neuroimaging.

Published
2019
Full Text
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41. Math for SPM

Author

Gau, Remi

Abstract

These slides were made and compiled by Joana Leitao from the Computational Cognitive Neuroimaging group from the University of Birmingham (UK).They cover some of the basic mathematical concepts necessary to understand fMRI analysis:- basic linear algebra- the ordinary least square solution of the general linear model- convolution and the brain as a linear time invariant system- examples of typical design matrices (t-test, ANOVA...)Over the years we have found them very useful and wanted to put them there hoping they could help others.

Published
2018
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43. Our brain, our sense and us

Author

Gau, Remi

Abstract

These are the slides I used for an interactive presentation given at the children section of the Skeptics in the Pub of Gravesend (England)

Published
2017
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44. SPM and some of its maths: an introduction

Author

Gau, Remi

Abstract

These slides were made and compiled by Joana Leitao from the Computational Cognitive Neuroimaging group from the University of Birmingham (UK).They cover some of the basic mathematical concepts necessary to understand fMRI analysis:- basic linear algebra- the ordinary least square solution of the general linear model- convolution and the brain as a linear time invariant system- examples of typical design matrices (t-test, ANOVA...)Over the years we have found them very useful and wanted to put them there hoping they could help others.

Published
2017
Full Text
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