QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data

Matthew Cieslak; Philip A Cook; Xiaosong He; Fang-Cheng Yeh; Thijs Dhollander; Azeez Adebimpe; Geoffrey K Aguirre; Danielle S Bassett; Richard F Betzel; Josiane Bourque; Laura M Cabral; Christos Davatzikos; John A Detre; Eric Earl; Mark A Elliott; Shreyas Fadnavis; Damien A Fair; Will Foran; Panagiotis Fotiadis; Eleftherios Garyfallidis; Barry Giesbrecht; Ruben C Gur; Raquel E Gur; Max B Kelz; Anisha Keshavan; Bart S Larsen; Beatriz Luna; Allyson P Mackey; Michael P Milham; Desmond J Oathes; Anders Perrone; Adam R Pines; David R Roalf; Adam Richie-Halford; Ariel Rokem; Valerie J Sydnor; Tinashe M Tapera; Ursula A Tooley; Jean M Vettel; Jason D Yeatman; Scott T Grafton; Theodore D Satterthwaite

doi:10.1038/s41592-021-01185-5

QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data

Nat Methods. 2021 Jul;18(7):775-778. doi: 10.1038/s41592-021-01185-5. Epub 2021 Jun 21.

Authors

Matthew Cieslak¹, Philip A Cook², Xiaosong He², Fang-Cheng Yeh³, Thijs Dhollander⁴, Azeez Adebimpe², Geoffrey K Aguirre², Danielle S Bassett², Richard F Betzel⁵, Josiane Bourque², Laura M Cabral³, Christos Davatzikos², John A Detre², Eric Earl⁶, Mark A Elliott², Shreyas Fadnavis⁵, Damien A Fair⁷, Will Foran³, Panagiotis Fotiadis², Eleftherios Garyfallidis⁵, Barry Giesbrecht⁸, Ruben C Gur², Raquel E Gur², Max B Kelz², Anisha Keshavan⁹, Bart S Larsen², Beatriz Luna³, Allyson P Mackey², Michael P Milham¹⁰, Desmond J Oathes², Anders Perrone^{6

7}, Adam R Pines², David R Roalf², Adam Richie-Halford⁹, Ariel Rokem⁹, Valerie J Sydnor², Tinashe M Tapera², Ursula A Tooley², Jean M Vettel¹¹, Jason D Yeatman¹², Scott T Grafton⁸, Theodore D Satterthwaite¹³

Affiliations

¹ University of Pennsylvania, Philadelphia, PA, USA. matthew.cieslak@pennmedicine.upenn.edu.
² University of Pennsylvania, Philadelphia, PA, USA.
³ University of Pittsburgh, Pittsburgh, PA, USA.
⁴ Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
⁵ Indiana University, Bloomington, IN, USA.
⁶ Oregon Health and Science University, Portland, OR, USA.
⁷ University of Minnesota, Minneapolis, MN, USA.
⁸ University of California, Santa Barbara, Santa Barbara, CA, USA.
⁹ University of Washington, Seattle, WA, USA.
¹⁰ Child Mind Institute, New York, NY, USA.
¹¹ Army Research Laboratoriess, Aberdeen, MD, USA.
¹² Stanford University, Stanford, CA, USA.
¹³ University of Pennsylvania, Philadelphia, PA, USA. sattertt@pennmedicine.upenn.edu.

Abstract

Diffusion-weighted magnetic resonance imaging (dMRI) is the primary method for noninvasively studying the organization of white matter in the human brain. Here we introduce QSIPrep, an integrative software platform for the processing of diffusion images that is compatible with nearly all dMRI sampling schemes. Drawing on a diverse set of software suites to capitalize on their complementary strengths, QSIPrep facilitates the implementation of best practices for processing of diffusion images.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Brain / diagnostic imaging*
Diffusion Magnetic Resonance Imaging / methods*
Humans
Image Processing, Computer-Assisted / methods*
Programming Languages
Software*
Workflow

Abstract

Publication types

MeSH terms

Grants and funding