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A Robust Modular Automated Neuroimaging Pipeline for Model Inputs to TheVirtualBrain

TheVirtualBrain, an open-source platform for large-scale network modeling, can be personalized to an individual using a wide range of neuroimaging modalities. With the growing number and scale of neuroimaging data sharing initiatives of both healthy and clinical populations comes an opportunity to c...

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Autores principales: Frazier-Logue, Noah, Wang, Justin, Wang, Zheng, Sodums, Devin, Khosla, Anisha, Samson, Alexandria D., McIntosh, Anthony R., Shen, Kelly
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9239912/
https://www.ncbi.nlm.nih.gov/pubmed/35784190
http://dx.doi.org/10.3389/fninf.2022.883223
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author Frazier-Logue, Noah
Wang, Justin
Wang, Zheng
Sodums, Devin
Khosla, Anisha
Samson, Alexandria D.
McIntosh, Anthony R.
Shen, Kelly
author_facet Frazier-Logue, Noah
Wang, Justin
Wang, Zheng
Sodums, Devin
Khosla, Anisha
Samson, Alexandria D.
McIntosh, Anthony R.
Shen, Kelly
author_sort Frazier-Logue, Noah
collection PubMed
description TheVirtualBrain, an open-source platform for large-scale network modeling, can be personalized to an individual using a wide range of neuroimaging modalities. With the growing number and scale of neuroimaging data sharing initiatives of both healthy and clinical populations comes an opportunity to create large and heterogeneous sets of dynamic network models to better understand individual differences in network dynamics and their impact on brain health. Here we present TheVirtualBrain-UK Biobank pipeline, a robust, automated and open-source brain image processing solution to address the expanding scope of TheVirtualBrain project. Our pipeline generates connectome-based modeling inputs compatible for use with TheVirtualBrain. We leverage the existing multimodal MRI processing pipeline from the UK Biobank made for use with a variety of brain imaging modalities. We add various features and changes to the original UK Biobank implementation specifically for informing large-scale network models, including user-defined parcellations for the construction of matching whole-brain functional and structural connectomes. Changes also include detailed reports for quality control of all modalities, a streamlined installation process, modular software packaging, updated software versions, and support for various publicly available datasets. The pipeline has been tested on various datasets from both healthy and clinical populations and is robust to the morphological changes observed in aging and dementia. In this paper, we describe these and other pipeline additions and modifications in detail, as well as how this pipeline fits into the TheVirtualBrain ecosystem.
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spelling pubmed-92399122022-06-30 A Robust Modular Automated Neuroimaging Pipeline for Model Inputs to TheVirtualBrain Frazier-Logue, Noah Wang, Justin Wang, Zheng Sodums, Devin Khosla, Anisha Samson, Alexandria D. McIntosh, Anthony R. Shen, Kelly Front Neuroinform Neuroscience TheVirtualBrain, an open-source platform for large-scale network modeling, can be personalized to an individual using a wide range of neuroimaging modalities. With the growing number and scale of neuroimaging data sharing initiatives of both healthy and clinical populations comes an opportunity to create large and heterogeneous sets of dynamic network models to better understand individual differences in network dynamics and their impact on brain health. Here we present TheVirtualBrain-UK Biobank pipeline, a robust, automated and open-source brain image processing solution to address the expanding scope of TheVirtualBrain project. Our pipeline generates connectome-based modeling inputs compatible for use with TheVirtualBrain. We leverage the existing multimodal MRI processing pipeline from the UK Biobank made for use with a variety of brain imaging modalities. We add various features and changes to the original UK Biobank implementation specifically for informing large-scale network models, including user-defined parcellations for the construction of matching whole-brain functional and structural connectomes. Changes also include detailed reports for quality control of all modalities, a streamlined installation process, modular software packaging, updated software versions, and support for various publicly available datasets. The pipeline has been tested on various datasets from both healthy and clinical populations and is robust to the morphological changes observed in aging and dementia. In this paper, we describe these and other pipeline additions and modifications in detail, as well as how this pipeline fits into the TheVirtualBrain ecosystem. Frontiers Media S.A. 2022-06-14 /pmc/articles/PMC9239912/ /pubmed/35784190 http://dx.doi.org/10.3389/fninf.2022.883223 Text en Copyright © 2022 Frazier-Logue, Wang, Wang, Sodums, Khosla, Samson, McIntosh and Shen. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Neuroscience
Frazier-Logue, Noah
Wang, Justin
Wang, Zheng
Sodums, Devin
Khosla, Anisha
Samson, Alexandria D.
McIntosh, Anthony R.
Shen, Kelly
A Robust Modular Automated Neuroimaging Pipeline for Model Inputs to TheVirtualBrain
title A Robust Modular Automated Neuroimaging Pipeline for Model Inputs to TheVirtualBrain
title_full A Robust Modular Automated Neuroimaging Pipeline for Model Inputs to TheVirtualBrain
title_fullStr A Robust Modular Automated Neuroimaging Pipeline for Model Inputs to TheVirtualBrain
title_full_unstemmed A Robust Modular Automated Neuroimaging Pipeline for Model Inputs to TheVirtualBrain
title_short A Robust Modular Automated Neuroimaging Pipeline for Model Inputs to TheVirtualBrain
title_sort robust modular automated neuroimaging pipeline for model inputs to thevirtualbrain
topic Neuroscience
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9239912/
https://www.ncbi.nlm.nih.gov/pubmed/35784190
http://dx.doi.org/10.3389/fninf.2022.883223
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