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Souter NE, Bhagwat N, Racey C, Wilkinson R, Duncan NW, Samuel G, Lannelongue L, Selvan R, Rae CL. Measuring and reducing the carbon footprint of fMRI preprocessing in fMRIPrep. Hum Brain Mapp 2024; 45:e70003. [PMID: 39185668 PMCID: PMC11345634 DOI: 10.1002/hbm.70003] [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: 04/15/2024] [Revised: 07/18/2024] [Accepted: 08/06/2024] [Indexed: 08/27/2024] Open
Abstract
Computationally expensive data processing in neuroimaging research places demands on energy consumption-and the resulting carbon emissions contribute to the climate crisis. We measured the carbon footprint of the functional magnetic resonance imaging (fMRI) preprocessing tool fMRIPrep, testing the effect of varying parameters on estimated carbon emissions and preprocessing performance. Performance was quantified using (a) statistical individual-level task activation in regions of interest and (b) mean smoothness of preprocessed data. Eight variants of fMRIPrep were run with 257 participants who had completed an fMRI stop signal task (the same data also used in the original validation of fMRIPrep). Some variants led to substantial reductions in carbon emissions without sacrificing data quality: for instance, disabling FreeSurfer surface reconstruction reduced carbon emissions by 48%. We provide six recommendations for minimising emissions without compromising performance. By varying parameters and computational resources, neuroimagers can substantially reduce the carbon footprint of their preprocessing. This is one aspect of our research carbon footprint over which neuroimagers have control and agency to act upon.
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Affiliation(s)
| | - Nikhil Bhagwat
- McConnell Brain Imaging Centre, The Neuro (Montreal Neurological Institute – Hospital)McGill UniversityMontrealQuebecCanada
| | - Chris Racey
- School of PsychologyUniversity of SussexBrightonUK
- Sussex NeuroscienceUniversity of SussexBrightonUK
| | - Reese Wilkinson
- Department of Physics and AstronomyUniversity of SussexBrightonUK
| | - Niall W. Duncan
- Graduate Institute of Mind, Brain and ConsciousnessTaipei Medical UniversityTaipeiTaiwan
| | - Gabrielle Samuel
- Department of Global Health and Social Medicine, King's College LondonLondonUK
| | - Loïc Lannelongue
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
- Victor Phillip Dahdaleh Heart and Lung Research InstituteUniversity of CambridgeCambridgeUK
- Health Data Research UK CambridgeWellcome Genome Campus and University of CambridgeCambridgeUK
| | - Raghavendra Selvan
- Department of Computer ScienceUniversity of CopenhagenCopenhagenDenmark
- Department of NeuroscienceUniversity of CopenhagenCopenhagenDenmark
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Lalani B, Gray S, Mitra-Ganguli T. Systems Thinking in an era of climate change: Does cognitive neuroscience hold the key to improving environmental decision making? A perspective on Climate-Smart Agriculture. Front Integr Neurosci 2023; 17:1145744. [PMID: 37181865 PMCID: PMC10174047 DOI: 10.3389/fnint.2023.1145744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/02/2023] [Indexed: 05/16/2023] Open
Abstract
Systems Thinking (ST) can be defined as a mental construct that recognises patterns and connections in a particular complex system to make the "best decision" possible. In the field of sustainable agriculture and climate change, higher degrees of ST are assumed to be associated with more successful adaptation strategies under changing conditions, and "better" environmental decision making in a number of environmental and cultural settings. Future climate change scenarios highlight the negative effects on agricultural productivity worldwide, particularly in low-income countries (LICs) situated in the Global South. Alongside this, current measures of ST are limited by their reliance on recall, and are prone to possible measurement errors. Using Climate-Smart Agriculture (CSA), as an example case study, in this article we explore: (i) ST from a social science perspective; (ii) cognitive neuroscience tools that could be used to explore ST abilities in the context of LICs; (iii) an exploration of the possible correlates of systems thinking: observational learning, prospective thinking/memory and the theory of planned behaviour and (iv) a proposed theory of change highlighting the integration of social science frameworks and a cognitive neuroscience perspective. We find, recent advancements in the field of cognitive neuroscience such as Near-Infrared Spectroscopy (NIRS) provide exciting potential to explore previously hidden forms of cognition, especially in a low-income country/field setting; improving our understanding of environmental decision-making and the ability to more accurately test more complex hypotheses where access to laboratory studies is severely limited. We highlight that ST may correlate with other key aspects involved in environmental decision-making and posit motivating farmers via specific brain networks would: (a) enhance understanding of CSA practices (e.g., via the frontoparietal network extending from the dorsolateral prefrontal cortex (DLPFC) to the parietal cortex (PC) a control hub involved in ST and observational learning) such as tailoring training towards developing improved ST abilities among farmers and involving observational learning more explicitly and (b) motivate farmers to use such practices [e.g., via the network between the DLPFC and nucleus accumbens (NAc)] which mediates reward processing and motivation by focussing on a reward/emotion to engage farmers. Finally, our proposed interdisciplinary theory of change can be used as a starting point to encourage discussion and guide future research in this space.
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Affiliation(s)
- Baqir Lalani
- Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
- *Correspondence: Baqir Lalani
| | - Steven Gray
- Department of Community Sustainability, Michigan State University, East Lansing, MI, United States
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3
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Mitchell JW, Noble A, Baker G, Batchelor R, Brigo F, Christensen J, French J, Gil-Nagel A, Guekht A, Jette N, Kälviäinen R, Leach JP, Maguire M, O’Brien T, Rosenow F, Ryvlin P, Tittensor P, Tripathi M, Trinka E, Wiebe S, Williamson PR, Marson T. Protocol for the development of an international Core Outcome Set for treatment trials in adults with epilepsy: the EPilepsy outcome Set for Effectiveness Trials Project (EPSET). Trials 2022; 23:943. [PMCID: PMC9670528 DOI: 10.1186/s13063-022-06729-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 09/12/2022] [Indexed: 11/19/2022] Open
Abstract
Background A Core Outcome Set (COS) is a standardised list of outcomes that should be reported as a minimum in all clinical trials. In epilepsy, the choice of outcomes varies widely among existing studies, particularly in clinical trials. This diminishes opportunities for informed decision-making, contributes to research waste and is a barrier to integrating findings in systematic reviews and meta-analyses. Furthermore, the outcomes currently being measured may not reflect what is important to people with epilepsy. Therefore, we aim to develop a COS specific to clinical effectiveness research for adults with epilepsy using Delphi consensus methodology. Methods The EPSET Study will comprise of three phases and follow the core methodological principles as outlined by the Core Outcome Measures in Effectiveness Trials (COMET) Initiative. Phase 1 will include two focused literature reviews to identify candidate outcomes from the qualitative literature and current outcome measurement practice in phase III and phase IV clinical trials. Phase 2 aims to achieve international consensus to define which outcomes should be measured as a minimum in future trials, using a Delphi process including an online consensus meeting involving key stakeholders. Phase 3 will involve dissemination of the ratified COS to facilitate uptake in future trials and the planning of further research to identify the most appropriate measurement instruments to use to capture the COS in research practice. Discussion Harmonising outcome measurement across future clinical trials should ensure that the outcomes measured are relevant to patients and health services, and allow for more meaningful results to be obtained. Core Outcome Set registration COMET Initiative as study 118.
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Affiliation(s)
- James W. Mitchell
- grid.10025.360000 0004 1936 8470Association of British Neurologists Clinical Research Fellow, Institute of Systems, Molecular and Integrative Biology (ISMIB), University of Liverpool, Liverpool, UK
| | - Adam Noble
- grid.10025.360000 0004 1936 8470Health Services Research, Institute of Population Health, Policy and Systems, University of Liverpool, Liverpool, UK
| | - Gus Baker
- grid.10025.360000 0004 1936 8470University of Liverpool, Liverpool, UK and Secretary General at International Bureau for Epilepsy, Sandyford, Dublin, Ireland
| | - Rachel Batchelor
- grid.4991.50000 0004 1936 8948The Oxford Institute of Clinical Psychology Training and Research, University of Oxford, Oxford, UK
| | - Francesco Brigo
- grid.513131.4Department of Neurology, Hospital of Merano (SABES-ASDAA), Merano-Meran, Italy
| | - Jakob Christensen
- grid.7048.b0000 0001 1956 2722Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jacqueline French
- grid.137628.90000 0004 1936 8753NYU Comprehensive Epilepsy Center, New York, USA
| | - Antonio Gil-Nagel
- grid.413297.a0000 0004 1768 8622Department of Neurology, Hospital Ruber Internacional, Madrid, Spain
| | - Alla Guekht
- grid.489325.1Moscow Research and Clinical Center for Neuropsychiatry, Moscow, Russia ,grid.78028.350000 0000 9559 0613Russian National Research Medical University, Moscow, Russia
| | - Nathalie Jette
- grid.59734.3c0000 0001 0670 2351Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Reetta Kälviäinen
- grid.410705.70000 0004 0628 207XUniversity of Eastern Finland and Kuopio Epilepsy Center, Kuopio University Hospital, Member of EpiCARE ERN, Kuopio, Finland
| | - John Paul Leach
- grid.8756.c0000 0001 2193 314XSchool of Medicine, Dentistry & Nursing, University of Glasgow, Glasgow, UK
| | - Melissa Maguire
- grid.9909.90000 0004 1936 8403Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Terence O’Brien
- grid.1002.30000 0004 1936 7857Central Clinical School, Monash University, Melbourne, Australia
| | - Felix Rosenow
- grid.411088.40000 0004 0578 8220Epilepsy Center Frankfurt-Rhine-Main, University Hospital Frankfurt, Goethe-University, Frankfurt, Germany
| | - Philippe Ryvlin
- grid.8515.90000 0001 0423 4662Department of Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Phil Tittensor
- grid.6374.60000000106935374The Royal Wolverhampton NHS Trust and Honorary Lecturer, University of Wolverhampton, Wolverhampton, UK
| | - Manjari Tripathi
- grid.413618.90000 0004 1767 6103Department of Neurology, Neurosciences Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Eugen Trinka
- grid.21604.310000 0004 0523 5263Department of Neurology, Christian Doppler University Hospital, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Samuel Wiebe
- grid.22072.350000 0004 1936 7697Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Paula R. Williamson
- grid.10025.360000 0004 1936 8470Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Tony Marson
- grid.10025.360000 0004 1936 8470Institute of Systems, Molecular and Integrative Biology (ISMIB), University of Liverpool, Liverpool, UK
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