Analysis of task-based functional MRI data preprocessed with fMRIPrep
Oscar Esteban
(1)
,
Rastko Ciric
(1)
,
Karolina Finc
(2)
,
Ross Blair
(1)
,
Christopher Markiewicz
(1)
,
Craig Moodie
(1)
,
James Kent
(3)
,
Mathias Goncalves
(4)
,
Elizabeth Dupre
(5)
,
Daniel Gomez
(6)
,
Zhifang Ye
(7)
,
Taylor Salo
(8)
,
Romain Valabregue
(9)
,
Inge Amlien
(10)
,
Franziskus Liem
(11)
,
Nir Jacoby
(12)
,
Hrvoje Stojić
(13)
,
Matthew Cieslak
(14)
,
Sebastian Urchs
(5)
,
Yaroslav Halchenko
(15)
,
Satrajit Ghosh
(4, 16)
,
Alejandro de la Vega
(17)
,
Tal Yarkoni
(17)
,
Jessey Wright
(1)
,
William Thompson
(1, 18)
,
Russell Poldrack
,
Krzysztof Gorgolewski
(1)
1
Stanford University
2 Nicolaus Copernicus University [Toruń]
3 University of Iowa [Iowa City]
4 McGovern Institute for Brain Research [Cambridge]
5 McGill University = Université McGill [Montréal, Canada]
6 Radboud University [Nijmegen]
7 BNU - Beijing Normal University
8 FIU - Florida International University [Miami]
9 ICM - Institut du Cerveau = Paris Brain Institute
10 UiO - University of Oslo
11 UZH - Universität Zürich [Zürich] = University of Zurich
12 Columbia University [New York]
13 UCL - University College of London [London]
14 University of Pennsylvania
15 Dartmouth College [Hanover]
16 HMS - Harvard Medical School [Boston]
17 University of Texas at Austin [Austin]
18 Karolinska Institutet [Stockholm]
2 Nicolaus Copernicus University [Toruń]
3 University of Iowa [Iowa City]
4 McGovern Institute for Brain Research [Cambridge]
5 McGill University = Université McGill [Montréal, Canada]
6 Radboud University [Nijmegen]
7 BNU - Beijing Normal University
8 FIU - Florida International University [Miami]
9 ICM - Institut du Cerveau = Paris Brain Institute
10 UiO - University of Oslo
11 UZH - Universität Zürich [Zürich] = University of Zurich
12 Columbia University [New York]
13 UCL - University College of London [London]
14 University of Pennsylvania
15 Dartmouth College [Hanover]
16 HMS - Harvard Medical School [Boston]
17 University of Texas at Austin [Austin]
18 Karolinska Institutet [Stockholm]
Karolina Finc
- Fonction : Auteur
- PersonId : 1382890
- ORCID : 0000-0002-0157-030X
Zhifang Ye
- Fonction : Auteur
- PersonId : 1382891
- ORCID : 0000-0003-0489-2619
Taylor Salo
- Fonction : Auteur
- PersonId : 1382892
- ORCID : 0000-0001-9813-3167
Nir Jacoby
- Fonction : Auteur
- PersonId : 1382893
- ORCID : 0000-0001-7936-9991
Sebastian Urchs
- Fonction : Auteur
- PersonId : 809753
- ORCID : 0000-0001-5504-8579
Satrajit Ghosh
- Fonction : Auteur
- PersonId : 1382894
- ORCID : 0000-0002-5312-6729
William Thompson
- Fonction : Auteur
- PersonId : 1382895
- ORCID : 0000-0002-0533-6035
Russell Poldrack
- Fonction : Auteur
- PersonId : 783513
- ORCID : 0000-0001-6755-0259
- IdRef : 165846089
Résumé
Functional magnetic resonance imaging (fMRI) is a standard tool to investigate the neural correlates of cognition. fMRI noninvasively measures brain activity, allowing identification of patterns evoked by tasks performed during scanning. Despite the long history of this technique, the idiosyncrasies of each dataset have led to the use of ad-hoc preprocessing protocols customized for nearly every different study. This approach is time consuming, error prone and unsuitable for combining datasets from many sources. Here we showcase fMRIPrep (http://fmriprep.org), a robust tool to prepare human fMRI data for statistical analysis. This software instrument addresses the reproducibility concerns of the established protocols for fMRI preprocessing. By leveraging the Brain Imaging Data Structure to standardize both the input datasets (MRI data as stored by the scanner) and the outputs (data ready for modeling and analysis), fMRIPrep is capable of preprocessing a diversity of datasets without manual intervention. In support of the growing popularity of fMRIPrep, this protocol describes how to integrate the tool in a task-based fMRI investigation workflow.