XCP-D: A Robust Pipeline for the post-processing of fMRI data

Kahini Mehta; Taylor Salo; Thomas Madison; Azeez Adebimpe; Danielle S Bassett; Max Bertolero; Matthew Cieslak; Sydney Covitz; Audrey Houghton; Arielle S Keller; Audrey Luo; Oscar Miranda-Dominguez; Steve M Nelson; Golia Shafiei; Sheila Shanmugan; Russell T Shinohara; Valerie J Sydnor; Eric Feczko; Damien A Fair; Theodore D Satterthwaite

doi:10.1101/2023.11.20.567926

XCP-D: A Robust Pipeline for the post-processing of fMRI data

bioRxiv [Preprint]. 2023 Nov 21:2023.11.20.567926. doi: 10.1101/2023.11.20.567926.

Authors

Kahini Mehta^{1

2

3}, Taylor Salo^{1

2

3}, Thomas Madison⁴, Azeez Adebimpe^{1

2

3}, Danielle S Bassett^{5

6

7

8

9}, Max Bertolero^{1

2

3}, Matthew Cieslak^{1

2

3}, Sydney Covitz^{1

2

3}, Audrey Houghton¹⁰, Arielle S Keller^{1

2

3}, Audrey Luo^{1

2

3}, Oscar Miranda-Dominguez^{4

10

11}, Steve M Nelson⁴, Golia Shafiei^{1

2

3}, Sheila Shanmugan^{1

2

3}, Russell T Shinohara^{12

13}, Valerie J Sydnor^{1

2

3}, Eric Feczko⁴, Damien A Fair^{4

10

11}, Theodore D Satterthwaite^{1

2

3

12

13}

Affiliations

¹ Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
² Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA.
³ Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
⁴ Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55454, USA.
⁵ Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, PA 19104, USA.
⁶ Department of Electrical & Systems Engineering, University of Pennsylvania, PA 19104, USA.
⁷ Department of Neurology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
⁸ Department of Physics & Astronomy, University of Pennsylvania, Philadelphia, PA, 19104, USA.
⁹ Santa Fe Institute, Santa Fe, NM, 87051, USA.
¹⁰ Masonic Institute for the Developing Brain, University of Minnesota Medical School, Minneapolis, MN, USA.
¹¹ Institute of Child Development, University of Minnesota Medical School, Minneapolis, MN, USA.
¹² Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
¹³ Center for Biomedical Image Computing and Analytics, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

Abstract

Functional neuroimaging is an essential tool for neuroscience research. Pre-processing pipelines produce standardized, minimally pre-processed data to support a range of potential analyses. However, post-processing is not similarly standardized. While several options for post-processing exist, they tend not to support output from disparate pre-processing pipelines, may have limited documentation, and may not follow BIDS best practices. Here we present XCP-D, which presents a solution to these issues. XCP-D is a collaborative effort between PennLINC at the University of Pennsylvania and the DCAN lab at the University at Minnesota. XCP-D uses an open development model on GitHub and incorporates continuous integration testing; it is distributed as a Docker container or Singularity image. XCP-D generates denoised BOLD images and functional derivatives from resting-state data in either NifTI or CIFTI files, following pre-processing with fMRIPrep, HCP, and ABCD-BIDS pipelines. Even prior to its official release, XCP-D has been downloaded >3,000 times from DockerHub. Together, XCP-D facilitates robust, scalable, and reproducible post-processing of fMRI data.

Keywords: denoising; fMRI; functional connectivity; image processing; post-processing; reproducibility; resting-state; software.

Publication types

Preprint

Abstract

Publication types

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