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QSIPrep: An integrative platform for preprocessing and reconstructing diffusion MRI

View ORCID ProfileMatthew Cieslak, Philip A. Cook, Xiaosong He, Fang-Cheng Yeh, View ORCID ProfileThijs Dhollander, Azeez Adebimpe, Geoffrey K. Aguirre, View ORCID ProfileDanielle S. Bassett, Richard F. Betzel, Josiane Bourque, Laura M. Cabral, Christos Davatzikos, John 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 Kelz, View ORCID ProfileAnisha Keshavan, Bart S. Larsen, Beatriz Luna, Allyson P. Mackey, Michael Milham, Desmond J. Oathes, Anders Perrone, Adam R. Pines, David R. Roalf, View ORCID ProfileAdam 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: https://doi.org/10.1101/2020.09.04.282269
Matthew Cieslak
1University of Pennsylvania, Philadelphia, PA
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  • For correspondence: matthew.cieslak@pennmedicine.upenn.edu
Philip A. Cook
1University of Pennsylvania, Philadelphia, PA
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Xiaosong He
1University of Pennsylvania, Philadelphia, PA
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Fang-Cheng Yeh
2University of Pittsburgh, Pittsburgh, PA
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Thijs Dhollander
3Murdoch Children’s Research Institute, Melbourne, VIC
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Azeez Adebimpe
1University of Pennsylvania, Philadelphia, PA
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Geoffrey K. Aguirre
1University of Pennsylvania, Philadelphia, PA
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Danielle S. Bassett
1University of Pennsylvania, Philadelphia, PA
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Richard F. Betzel
4Indiana University, Bloomington, IN
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Josiane Bourque
1University of Pennsylvania, Philadelphia, PA
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Laura M. Cabral
2University of Pittsburgh, Pittsburgh, PA
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Christos Davatzikos
1University of Pennsylvania, Philadelphia, PA
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John Detre
1University of Pennsylvania, Philadelphia, PA
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Eric Earl
5Oregon Health and Science University, Portland, OR
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Mark A. Elliott
1University of Pennsylvania, Philadelphia, PA
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Shreyas Fadnavis
4Indiana University, Bloomington, IN
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Damien A. Fair
5Oregon Health and Science University, Portland, OR
6University of Minnesota, Minneapolis, MN
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Will Foran
2University of Pittsburgh, Pittsburgh, PA
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Panagiotis Fotiadis
1University of Pennsylvania, Philadelphia, PA
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Eleftherios Garyfallidis
4Indiana University, Bloomington, IN
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Barry Giesbrecht
7University of California, Santa Barbara, Santa Barbara, CA
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Ruben C. Gur
1University of Pennsylvania, Philadelphia, PA
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Raquel E. Gur
1University of Pennsylvania, Philadelphia, PA
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Max Kelz
1University of Pennsylvania, Philadelphia, PA
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Anisha Keshavan
9University of Washington, Seattle WA
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Bart S. Larsen
1University of Pennsylvania, Philadelphia, PA
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Beatriz Luna
2University of Pittsburgh, Pittsburgh, PA
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Allyson P. Mackey
1University of Pennsylvania, Philadelphia, PA
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Michael Milham
10Child Mind Institute, New York, NY
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Desmond J. Oathes
1University of Pennsylvania, Philadelphia, PA
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Anders Perrone
5Oregon Health and Science University, Portland, OR
6University of Minnesota, Minneapolis, MN
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Adam R. Pines
1University of Pennsylvania, Philadelphia, PA
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David R. Roalf
1University of Pennsylvania, Philadelphia, PA
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Adam Richie-Halford
9University of Washington, Seattle WA
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Ariel Rokem
9University of Washington, Seattle WA
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Valerie J. Sydnor
1University of Pennsylvania, Philadelphia, PA
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Tinashe M. Tapera
1University of Pennsylvania, Philadelphia, PA
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Ursula A. Tooley
1University of Pennsylvania, Philadelphia, PA
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Jean M. Vettel
8Army Research Labs, Aberdeen, MD
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Jason D. Yeatman
11Stanford University, Stanford, CA
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Scott T. Grafton
7University of California, Santa Barbara, Santa Barbara, CA
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Theodore D. Satterthwaite
1University of Pennsylvania, Philadelphia, PA
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ABSTRACT

Diffusion-weighted magnetic resonance imaging (dMRI) has become the primary method for non-invasively studying the organization of white matter in the human brain. While many dMRI acquisition sequences have been developed, they all sample q-space in order to characterize water diffusion. Numerous software platforms have been developed for processing dMRI data, but most work on only a subset of sampling schemes or implement only parts of the processing workflow. Reproducible research and comparisons across dMRI methods are hindered by incompatible software, diverse file formats, and inconsistent naming conventions. Here we introduce QSIPrep, an integrative software platform for the processing of diffusion images that is compatible with nearly all dMRI sampling schemes. Drawing upon a diverse set of software suites to capitalize upon their complementary strengths, QSIPrep automatically applies best practices for dMRI preprocessing, including denoising, distortion correction, head motion correction, coregistration, and spatial normalization. Throughout, QSIPrep provides both visual and quantitative measures of data quality as well as “glass-box” methods reporting. Taken together, these features facilitate easy implementation of best practices for processing of diffusion images while simultaneously ensuring reproducibility.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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QSIPrep: An integrative platform for preprocessing and reconstructing diffusion MRI
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 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 Kelz, Anisha Keshavan, Bart S. Larsen, Beatriz Luna, Allyson P. Mackey, Michael 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
bioRxiv 2020.09.04.282269; doi: https://doi.org/10.1101/2020.09.04.282269
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QSIPrep: An integrative platform for preprocessing and reconstructing diffusion MRI
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 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 Kelz, Anisha Keshavan, Bart S. Larsen, Beatriz Luna, Allyson P. Mackey, Michael 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
bioRxiv 2020.09.04.282269; doi: https://doi.org/10.1101/2020.09.04.282269

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