Literature DB >> 34155395

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

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 Perrone6,7, 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.   

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.

Entities:  

Mesh：

Year:  2021        PMID： 34155395      PMCID： PMC8596781          DOI： 10.1038/s41592-021-01185-5

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   47.990


  34 in total

1.  NODDI: practical in vivo neurite orientation dispersion and density imaging of the human brain.

Authors:  Hui Zhang; Torben Schneider; Claudia A Wheeler-Kingshott; Daniel C Alexander
Journal:  Neuroimage       Date:  2012-03-30       Impact factor: 6.556

2.  MAPL: Tissue microstructure estimation using Laplacian-regularized MAP-MRI and its application to HCP data.

Authors:  Rutger H J Fick; Demian Wassermann; Emmanuel Caruyer; Rachid Deriche
Journal:  Neuroimage       Date:  2016-04-01       Impact factor: 6.556

3.  N4ITK: improved N3 bias correction.

Authors:  Nicholas J Tustison; Brian B Avants; Philip A Cook; Yuanjie Zheng; Alexander Egan; Paul A Yushkevich; James C Gee
Journal:  IEEE Trans Med Imaging       Date:  2010-04-08       Impact factor: 10.048

Review 4.  Neuroimaging of the Philadelphia neurodevelopmental cohort.

Authors:  Theodore D Satterthwaite; Mark A Elliott; Kosha Ruparel; James Loughead; Karthik Prabhakaran; Monica E Calkins; Ryan Hopson; Chad Jackson; Jack Keefe; Marisa Riley; Frank D Mentch; Patrick Sleiman; Ragini Verma; Christos Davatzikos; Hakon Hakonarson; Ruben C Gur; Raquel E Gur
Journal:  Neuroimage       Date:  2013-08-03       Impact factor: 6.556

5.  Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in python.

Authors:  Krzysztof Gorgolewski; Christopher D Burns; Cindee Madison; Dav Clark; Yaroslav O Halchenko; Michael L Waskom; Satrajit S Ghosh
Journal:  Front Neuroinform       Date:  2011-08-22       Impact factor: 4.081

6.  Mean apparent propagator (MAP) MRI: a novel diffusion imaging method for mapping tissue microstructure.

Authors:  Evren Özarslan; Cheng Guan Koay; Timothy M Shepherd; Michal E Komlosh; M Okan İrfanoğlu; Carlo Pierpaoli; Peter J Basser
Journal:  Neuroimage       Date:  2013-04-13       Impact factor: 6.556

7.  Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain.

Authors:  B B Avants; C L Epstein; M Grossman; J C Gee
Journal:  Med Image Anal       Date:  2007-06-23       Impact factor: 8.545

8.  The impact of quality assurance assessment on diffusion tensor imaging outcomes in a large-scale population-based cohort.

Authors:  David R Roalf; Megan Quarmley; Mark A Elliott; Theodore D Satterthwaite; Simon N Vandekar; Kosha Ruparel; Efstathios D Gennatas; Monica E Calkins; Tyler M Moore; Ryan Hopson; Karthik Prabhakaran; Chad T Jackson; Ragini Verma; Hakon Hakonarson; Ruben C Gur; Raquel E Gur
Journal:  Neuroimage       Date:  2015-10-28       Impact factor: 6.556

9.  An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging.

Authors:  Jesper L R Andersson; Stamatios N Sotiropoulos
Journal:  Neuroimage       Date:  2015-10-20       Impact factor: 6.556

10.  fMRIPrep: a robust preprocessing pipeline for functional MRI.

Authors:  Russell A Poldrack; Krzysztof J Gorgolewski; 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
Journal:  Nat Methods       Date:  2018-12-10       Impact factor: 28.547
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  22 in total

Review 1.  Tractography methods and findings in brain tumors and traumatic brain injury.

Authors:  Fang-Cheng Yeh; Andrei Irimia; Dhiego Chaves de Almeida Bastos; Alexandra J Golby
Journal:  Neuroimage       Date:  2021-10-18       Impact factor: 6.556

2.  White Matter Characteristics of Damage Along Fiber Tracts in Patients with Type 2 Diabetes Mellitus.

Authors:  Haoming Huang; Xiaomeng Ma; Xiaomei Yue; Shangyu Kang; Yifan Li; Yawen Rao; Yue Feng; Jinjian Wu; Wenjie Long; Yuna Chen; Wenjiao Lyu; Xin Tan; Shijun Qiu
Journal:  Clin Neuroradiol       Date:  2022-09-16       Impact factor: 3.156

3.  ASLPrep: a platform for processing of arterial spin labeled MRI and quantification of regional brain perfusion.

Authors:  Azeez Adebimpe; Maxwell Bertolero; Sudipto Dolui; Matthew Cieslak; Kristin Murtha; Erica B Baller; Bradley Boeve; Adam Boxer; Ellyn R Butler; Phil Cook; Stan Colcombe; Sydney Covitz; Christos Davatzikos; Diego G Davila; Mark A Elliott; Matthew W Flounders; Alexandre R Franco; Raquel E Gur; Ruben C Gur; Basma Jaber; Corey McMillian; Michael Milham; Henk J M M Mutsaerts; Desmond J Oathes; Christopher A Olm; Jeffrey S Phillips; Will Tackett; David R Roalf; Howard Rosen; Tinashe M Tapera; M Dylan Tisdall; Dale Zhou; Oscar Esteban; Russell A Poldrack; John A Detre; Theodore D Satterthwaite
Journal:  Nat Methods       Date:  2022-06-10       Impact factor: 47.990

4.  Cortical-subcortical structural connections support transcranial magnetic stimulation engagement of the amygdala.

Authors:  Valerie J Sydnor; Matthew Cieslak; Romain Duprat; Joseph Deluisi; Matthew W Flounders; Hannah Long; Morgan Scully; Nicholas L Balderston; Yvette I Sheline; Dani S Bassett; Theodore D Satterthwaite; Desmond J Oathes
Journal:  Sci Adv       Date:  2022-06-22       Impact factor: 14.957

Review 5.  Mapping the human connectome using diffusion MRI at 300 mT/m gradient strength: Methodological advances and scientific impact.

Authors:  Qiuyun Fan; Cornelius Eichner; Maryam Afzali; Lars Mueller; Chantal M W Tax; Mathias Davids; Mirsad Mahmutovic; Boris Keil; Berkin Bilgic; Kawin Setsompop; Hong-Hsi Lee; Qiyuan Tian; Chiara Maffei; Gabriel Ramos-Llordén; Aapo Nummenmaa; Thomas Witzel; Anastasia Yendiki; Yi-Qiao Song; Chu-Chung Huang; Ching-Po Lin; Nikolaus Weiskopf; Alfred Anwander; Derek K Jones; Bruce R Rosen; Lawrence L Wald; Susie Y Huang
Journal:  Neuroimage       Date:  2022-02-23       Impact factor: 7.400

Review 6.  What's new and what's next in diffusion MRI preprocessing.

Authors:  Chantal M W Tax; Matteo Bastiani; Jelle Veraart; Eleftherios Garyfallidis; M Okan Irfanoglu
Journal:  Neuroimage       Date:  2021-12-26       Impact factor: 7.400

7.  Local structure-function relationships in human brain networks across the lifespan.

Authors:  Farnaz Zamani Esfahlani; Joshua Faskowitz; Jonah Slack; Bratislav Mišić; Richard F Betzel
Journal:  Nat Commun       Date:  2022-04-19       Impact factor: 17.694

8.  PreQual: An automated pipeline for integrated preprocessing and quality assurance of diffusion weighted MRI images.

Authors:  Leon Y Cai; Qi Yang; Colin B Hansen; Vishwesh Nath; Karthik Ramadass; Graham W Johnson; Benjamin N Conrad; Brian D Boyd; John P Begnoche; Lori L Beason-Held; Andrea T Shafer; Susan M Resnick; Warren D Taylor; Gavin R Price; Victoria L Morgan; Baxter P Rogers; Kurt G Schilling; Bennett A Landman
Journal:  Magn Reson Med       Date:  2021-02-03       Impact factor: 3.737

9.  Lower fractional anisotropy of the corticothalamic tract and increased response time variability in adult patients with ADHD.

Authors:  Markus Kölle; Sarah Mackert; Katharina Heckel; Alexandra Philipsen; Martin Ulrich; Georg Grön
Journal:  J Psychiatry Neurosci       Date:  2022-03-17       Impact factor: 5.699

10.  FlywheelTools: Data Curation and Manipulation on the Flywheel Platform.

Authors:  Tinashe M Tapera; Matthew Cieslak; Max Bertolero; Azeez Adebimpe; Geoffrey K Aguirre; Ellyn R Butler; Philip A Cook; Diego Davila; Mark A Elliott; Sophia Linguiti; Kristin Murtha; William Tackett; John A Detre; Theodore D Satterthwaite
Journal:  Front Neuroinform       Date:  2021-06-22       Impact factor: 4.081
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