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FMRIPrep: a robust preprocessing pipeline for functional MRI

View ORCID ProfileOscar Esteban, View ORCID ProfileChristopher J. Markiewicz, Ross W. Blair, View ORCID ProfileCraig A. Moodie, View ORCID ProfileA. Ilkay Isik, View ORCID ProfileAsier Erramuzpe, View ORCID ProfileJames D. Kent, View ORCID ProfileMathias Goncalves, View ORCID ProfileElizabeth DuPre, Madeleine Snyder, View ORCID ProfileHiroyuki Oya, View ORCID ProfileSatrajit S. Ghosh, Jessey Wright, View ORCID ProfileJoke Durnez, View ORCID ProfileRussell A. Poldrack, View ORCID ProfileKrzysztof J. Gorgolewski
doi: https://doi.org/10.1101/306951
Oscar Esteban
1Department of Psychology, Stanford University, California, USA;
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  • For correspondence: phd@oscaresteban.es krzysztof.gorgolewski@gmail.com
Christopher J. Markiewicz
1Department of Psychology, Stanford University, California, USA;
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Ross W. Blair
1Department of Psychology, Stanford University, California, USA;
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Craig A. Moodie
2Medical School Center, Stanford University, California, USA;
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A. Ilkay Isik
3Max Planck Institute for Empirical Aesthetics, Hesse, Germany;
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Asier Erramuzpe
4Computational Neuroimaging Lab, Biocruces Health Research Institute, Bilbao, Spain;
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James D. Kent
5Neuroscience Program, University of Iowa, USA;
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Mathias Goncalves
6McGovern Institute for Brain Research, Massachusetts Institute of Technology: MIT, Cambridge, MA, USA;
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Elizabeth DuPre
7Montreal Neurological Institute, McGill University;
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Madeleine Snyder
8Department of Psychiatry, Stanford Medical School, Stanford University, California, USA;
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Hiroyuki Oya
9Department of Neurosurgery, University of Iowa Health Care, Iowa City, Iowa;
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Satrajit S. Ghosh
6McGovern Institute for Brain Research, Massachusetts Institute of Technology: MIT, Cambridge, MA, USA;
10Department of Otolaryngology, Harvard Medical School, Boston, MA, USA
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Jessey Wright
1Department of Psychology, Stanford University, California, USA;
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Joke Durnez
1Department of Psychology, Stanford University, California, USA;
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Russell A. Poldrack
1Department of Psychology, Stanford University, California, USA;
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Krzysztof J. Gorgolewski
1Department of Psychology, Stanford University, California, USA;
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  • For correspondence: phd@oscaresteban.es krzysztof.gorgolewski@gmail.com
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Abstract

Preprocessing of functional MRI (fMRI) involves numerous steps to clean and standardize data before statistical analysis. Generally, researchers create ad hoc preprocessing workflows for each new dataset, building upon a large inventory of tools available for each step. The complexity of these workflows has snowballed with rapid advances in MR data acquisition and image processing techniques. We introduce fMRIPrep, an analysis-agnostic tool that addresses the challenge of robust and reproducible preprocessing for task-based and resting fMRI data. FMRIPrep automatically adapts a best-in-breed workflow to the idiosyncrasies of virtually any dataset, ensuring high-quality preprocessing with no manual intervention. By introducing visual assessment checkpoints into an iterative integration framework for software-testing, we show that fMRIPrep robustly produces high-quality results on a diverse fMRI data collection comprising participants from 54 different studies in the OpenfMRI repository. We review the distinctive features of fMRIPrep in a qualitative comparison to other preprocessing workflows. We demonstrate that fMRIPrep achieves higher spatial accuracy as it introduces less uncontrolled spatial smoothness than commonly used preprocessing tools. FMRIPrep has the potential to transform fMRI research by equipping neuroscientists with a high-quality, robust, easy-to-use and transparent preprocessing workflow which can help ensure the validity of inference and the interpretability of their results.

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Posted July 24, 2018.
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FMRIPrep: a robust preprocessing pipeline for functional MRI
Oscar Esteban, Christopher J. Markiewicz, Ross W. Blair, Craig A. Moodie, A. Ilkay Isik, Asier Erramuzpe, James D. Kent, Mathias Goncalves, Elizabeth DuPre, Madeleine Snyder, Hiroyuki Oya, Satrajit S. Ghosh, Jessey Wright, Joke Durnez, Russell A. Poldrack, Krzysztof J. Gorgolewski
bioRxiv 306951; doi: https://doi.org/10.1101/306951
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FMRIPrep: a robust preprocessing pipeline for functional MRI
Oscar Esteban, Christopher J. Markiewicz, Ross W. Blair, Craig A. Moodie, A. Ilkay Isik, Asier Erramuzpe, James D. Kent, Mathias Goncalves, Elizabeth DuPre, Madeleine Snyder, Hiroyuki Oya, Satrajit S. Ghosh, Jessey Wright, Joke Durnez, Russell A. Poldrack, Krzysztof J. Gorgolewski
bioRxiv 306951; doi: https://doi.org/10.1101/306951

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