Cargando…

The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data

Quantifying, controlling, and monitoring image quality is an essential prerequisite for ensuring the validity and reproducibility of many types of neuroimaging data analyses. Implementation of quality control (QC) procedures is the key to ensuring that neuroimaging data are of high-quality and their...

Descripción completa

Detalles Bibliográficos
Autores principales: Kim, Hosung, Irimia, Andrei, Hobel, Samuel M., Pogosyan, Mher, Tang, Haoteng, Petrosyan, Petros, Blanco, Rita Esquivel Castelo, Duffy, Ben A., Zhao, Lu, Crawford, Karen L., Liew, Sook-Lei, Clark, Kristi, Law, Meng, Mukherjee, Pratik, Manley, Geoffrey T., Van Horn, John D., Toga, Arthur W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6722229/
https://www.ncbi.nlm.nih.gov/pubmed/31555116
http://dx.doi.org/10.3389/fninf.2019.00060
_version_ 1783448490858250240
author Kim, Hosung
Irimia, Andrei
Hobel, Samuel M.
Pogosyan, Mher
Tang, Haoteng
Petrosyan, Petros
Blanco, Rita Esquivel Castelo
Duffy, Ben A.
Zhao, Lu
Crawford, Karen L.
Liew, Sook-Lei
Clark, Kristi
Law, Meng
Mukherjee, Pratik
Manley, Geoffrey T.
Van Horn, John D.
Toga, Arthur W.
author_facet Kim, Hosung
Irimia, Andrei
Hobel, Samuel M.
Pogosyan, Mher
Tang, Haoteng
Petrosyan, Petros
Blanco, Rita Esquivel Castelo
Duffy, Ben A.
Zhao, Lu
Crawford, Karen L.
Liew, Sook-Lei
Clark, Kristi
Law, Meng
Mukherjee, Pratik
Manley, Geoffrey T.
Van Horn, John D.
Toga, Arthur W.
author_sort Kim, Hosung
collection PubMed
description Quantifying, controlling, and monitoring image quality is an essential prerequisite for ensuring the validity and reproducibility of many types of neuroimaging data analyses. Implementation of quality control (QC) procedures is the key to ensuring that neuroimaging data are of high-quality and their validity in the subsequent analyses. We introduce the QC system of the Laboratory of Neuro Imaging (LONI): a web-based system featuring a workflow for the assessment of various modality and contrast brain imaging data. The design allows users to anonymously upload imaging data to the LONI-QC system. It then computes an exhaustive set of QC metrics which aids users to perform a standardized QC by generating a range of scalar and vector statistics. These procedures are performed in parallel using a large compute cluster. Finally, the system offers an automated QC procedure for structural MRI, which can flag each QC metric as being ‘good’ or ‘bad.’ Validation using various sets of data acquired from a single scanner and from multiple sites demonstrated the reproducibility of our QC metrics, and the sensitivity and specificity of the proposed Auto QC to ‘bad’ quality images in comparison to visual inspection. To the best of our knowledge, LONI-QC is the first online QC system that uniquely supports the variety of functionality where we compute numerous QC metrics and perform visual/automated image QC of multi-contrast and multi-modal brain imaging data. The LONI-QC system has been used to assess the quality of large neuroimaging datasets acquired as part of various multi-site studies such as the Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Study and the Alzheimer’s Disease Neuroimaging Initiative (ADNI). LONI-QC’s functionality is freely available to users worldwide and its adoption by imaging researchers is likely to contribute substantially to upholding high standards of brain image data quality and to implementing these standards across the neuroimaging community.
format Online
Article
Text
id pubmed-6722229
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-67222292019-09-25 The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data Kim, Hosung Irimia, Andrei Hobel, Samuel M. Pogosyan, Mher Tang, Haoteng Petrosyan, Petros Blanco, Rita Esquivel Castelo Duffy, Ben A. Zhao, Lu Crawford, Karen L. Liew, Sook-Lei Clark, Kristi Law, Meng Mukherjee, Pratik Manley, Geoffrey T. Van Horn, John D. Toga, Arthur W. Front Neuroinform Neuroscience Quantifying, controlling, and monitoring image quality is an essential prerequisite for ensuring the validity and reproducibility of many types of neuroimaging data analyses. Implementation of quality control (QC) procedures is the key to ensuring that neuroimaging data are of high-quality and their validity in the subsequent analyses. We introduce the QC system of the Laboratory of Neuro Imaging (LONI): a web-based system featuring a workflow for the assessment of various modality and contrast brain imaging data. The design allows users to anonymously upload imaging data to the LONI-QC system. It then computes an exhaustive set of QC metrics which aids users to perform a standardized QC by generating a range of scalar and vector statistics. These procedures are performed in parallel using a large compute cluster. Finally, the system offers an automated QC procedure for structural MRI, which can flag each QC metric as being ‘good’ or ‘bad.’ Validation using various sets of data acquired from a single scanner and from multiple sites demonstrated the reproducibility of our QC metrics, and the sensitivity and specificity of the proposed Auto QC to ‘bad’ quality images in comparison to visual inspection. To the best of our knowledge, LONI-QC is the first online QC system that uniquely supports the variety of functionality where we compute numerous QC metrics and perform visual/automated image QC of multi-contrast and multi-modal brain imaging data. The LONI-QC system has been used to assess the quality of large neuroimaging datasets acquired as part of various multi-site studies such as the Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Study and the Alzheimer’s Disease Neuroimaging Initiative (ADNI). LONI-QC’s functionality is freely available to users worldwide and its adoption by imaging researchers is likely to contribute substantially to upholding high standards of brain image data quality and to implementing these standards across the neuroimaging community. Frontiers Media S.A. 2019-08-28 /pmc/articles/PMC6722229/ /pubmed/31555116 http://dx.doi.org/10.3389/fninf.2019.00060 Text en Copyright © 2019 Kim, Irimia, Hobel, Pogosyan, Tang, Petrosyan, Esquivel Castelo Blanco, Duffy, Zhao, Crawford, Liew, Clark, Law, Mukherjee, Manley, Van Horn and Toga. http://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
Kim, Hosung
Irimia, Andrei
Hobel, Samuel M.
Pogosyan, Mher
Tang, Haoteng
Petrosyan, Petros
Blanco, Rita Esquivel Castelo
Duffy, Ben A.
Zhao, Lu
Crawford, Karen L.
Liew, Sook-Lei
Clark, Kristi
Law, Meng
Mukherjee, Pratik
Manley, Geoffrey T.
Van Horn, John D.
Toga, Arthur W.
The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data
title The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data
title_full The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data
title_fullStr The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data
title_full_unstemmed The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data
title_short The LONI QC System: A Semi-Automated, Web-Based and Freely-Available Environment for the Comprehensive Quality Control of Neuroimaging Data
title_sort loni qc system: a semi-automated, web-based and freely-available environment for the comprehensive quality control of neuroimaging data
topic Neuroscience
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6722229/
https://www.ncbi.nlm.nih.gov/pubmed/31555116
http://dx.doi.org/10.3389/fninf.2019.00060
work_keys_str_mv AT kimhosung theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT irimiaandrei theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT hobelsamuelm theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT pogosyanmher theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT tanghaoteng theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT petrosyanpetros theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT blancoritaesquivelcastelo theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT duffybena theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT zhaolu theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT crawfordkarenl theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT liewsooklei theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT clarkkristi theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT lawmeng theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT mukherjeepratik theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT manleygeoffreyt theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT vanhornjohnd theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT togaarthurw theloniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT kimhosung loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT irimiaandrei loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT hobelsamuelm loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT pogosyanmher loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT tanghaoteng loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT petrosyanpetros loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT blancoritaesquivelcastelo loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT duffybena loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT zhaolu loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT crawfordkarenl loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT liewsooklei loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT clarkkristi loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT lawmeng loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT mukherjeepratik loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT manleygeoffreyt loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT vanhornjohnd loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata
AT togaarthurw loniqcsystemasemiautomatedwebbasedandfreelyavailableenvironmentforthecomprehensivequalitycontrolofneuroimagingdata