ModelArray: An R package for statistical analysis of fixel-wise data.

Humans White Matter Diffusion Magnetic Resonance Imaging / methods Software Research Design Models, Statistical
Big data Development Fixel-based analysis MRI Software Statistical analysis

Journal

NeuroImage
ISSN: 1095-9572
Titre abrégé: Neuroimage
Pays: United States
ID NLM: 9215515

Informations de publication

Date de publication:
01 05 2023
Historique:
received: 11 07 2022
revised: 08 03 2023
accepted: 14 03 2023
medline: 7 4 2023
pubmed: 18 3 2023
entrez: 17 3 2023
Statut: ppublish

Résumé

Diffusion MRI is the dominant non-invasive imaging method used to characterize white matter organization in health and disease. Increasingly, fiber-specific properties within a voxel are analyzed using fixels. While tools for conducting statistical analyses of fixel-wise data exist, currently available tools support only a limited number of statistical models. Here we introduce ModelArray, an R package for mass-univariate statistical analysis of fixel-wise data. At present, ModelArray supports linear models as well as generalized additive models (GAMs), which are particularly useful for studying nonlinear effects in lifespan data. In addition, ModelArray also aims for scalable analysis. With only several lines of code, even large fixel-wise datasets can be analyzed using a standard personal computer. Detailed memory profiling revealed that ModelArray required only limited memory even for large datasets. As an example, we applied ModelArray to fixel-wise data derived from diffusion images acquired as part of the Philadelphia Neurodevelopmental Cohort (n = 938). ModelArray revealed anticipated nonlinear developmental effects in white matter. Moving forward, ModelArray is supported by an open-source software development model that can incorporate additional statistical models and other imaging data types. Taken together, ModelArray provides a flexible and efficient platform for statistical analysis of fixel-wise data.

Identifiants

DOI: 10.1016/j.neuroimage.2023.120037 PMID: 36931330 PMC: PMC10119782
pubmed: 36931330
pii: S1053-8119(23)00183-0
doi: 10.1016/j.neuroimage.2023.120037
pmc: PMC10119782
mid: NIHMS1888963
pii:
doi:

Types de publication

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

Langues

eng

Sous-ensembles de citation

IM

Pagination

120037

Subventions

Organisme : NIMH NIH HHS
ID : RF1 MH121867
Pays : United States
Organisme : NIMH NIH HHS
ID : R37 MH125829
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH123550
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH120482
Pays : United States
Organisme : NIMH NIH HHS
ID : RF1 MH116920
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH113550
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH120174
Pays : United States
Organisme : NINDS NIH HHS
ID : R01 NS085211
Pays : United States
Organisme : NIDCD NIH HHS
ID : T32 DC000038
Pays : United States
Organisme : NIMH NIH HHS
ID : K99 MH127293
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH119185
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH112847
Pays : United States
Organisme : NIBIB NIH HHS
ID : R01 EB022573
Pays : United States
Organisme : NINDS NIH HHS
ID : R01 NS112274
Pays : United States

Informations de copyright

Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.

Références

Neuroimage. 2014 Feb 1;86:544-53
pubmed: 23921101
Neuroimage. 2017 Jan 1;144(Pt A):58-73
pubmed: 27639350
Neuroimage. 2009 Jan 1;44(1):83-98
pubmed: 18501637
Nature. 2022 Mar;603(7902):654-660
pubmed: 35296861
Neuroimage. 2016 Nov 15;142:394-406
pubmed: 27523449
Nature. 2022 Apr;604(7906):525-533
pubmed: 35388223
Neuroimage. 2021 Nov 1;241:118417
pubmed: 34298083
Neuroimage. 2013 Oct 15;80:62-79
pubmed: 23684880
Neuroimage. 2019 Nov 15;202:116137
pubmed: 31473352
Magn Reson Imaging. 2019 Apr;57:194-209
pubmed: 30503948
IEEE Trans Med Imaging. 2010 Jun;29(6):1310-20
pubmed: 20378467
Nat Commun. 2022 May 12;13(1):2647
pubmed: 35551181
Magn Reson Med. 2016 Nov;76(5):1574-1581
pubmed: 26745823
Neuroimage. 2016 Jan 15;125:1063-1078
pubmed: 26481672
Neuroimage. 2012 Mar;60(1):340-52
pubmed: 22178809
Dev Cogn Neurosci. 2020 Oct;45:100853
pubmed: 32932204
Neuroimage. 2014 May 15;92:381-97
pubmed: 24530839
J Magn Reson B. 1996 Jun;111(3):209-19
pubmed: 8661285
Nat Methods. 2021 Jul;18(7):775-778
pubmed: 34155395
Hum Brain Mapp. 2013 Nov;34(11):2747-66
pubmed: 22611035
Sci Data. 2017 Dec 19;4:170181
pubmed: 29257126
Dev Cogn Neurosci. 2022 Dec;58:101171
pubmed: 36372005
Neuroimage. 2016 Jan 15;125:903-919
pubmed: 26520775
Neuroimage. 2021 Feb 1;226:117598
pubmed: 33249215
Neuroimage. 2015 Aug 15;117:40-55
pubmed: 26004503
PLoS One. 2013 Nov 15;8(11):e80713
pubmed: 24348913
Magn Reson Med. 2017 Jan;77(1):285-299
pubmed: 26822700
Neuroimage. 2016 Nov 1;141:556-572
pubmed: 27393418

Auteurs

Chenying Zhao (C)

Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Tinashe M Tapera (TM)

Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Joëlle Bagautdinova (J)

Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Josiane Bourque (J)

Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Sydney Covitz (S)

Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Raquel E Gur (RE)

Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Ruben C Gur (RC)

Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Bart Larsen (B)

Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Kahini Mehta (K)

Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Steven L Meisler (SL)

Program in Speech and Hearing Bioscience and Technology, Harvard University, Cambridge, MA 02139, USA.

Kristin Murtha (K)

Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

John Muschelli (J)

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.

David R Roalf (DR)

Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Valerie J Sydnor (VJ)

Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Alessandra M Valcarcel (AM)

Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA.

Russell T Shinohara (RT)

Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104, USA.

Matthew Cieslak (M)

Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Theodore D Satterthwaite (TD)

Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA; Penn/CHOP Lifespan Brain Institute, Perelman School of Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: sattertt@pennmedicine.upenn.edu.

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