{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T04:41:05Z","timestamp":1774586465981,"version":"3.50.1"},"reference-count":65,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,4,5]],"date-time":"2023-04-05T00:00:00Z","timestamp":1680652800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Neuroinform."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Neuroimaging technology has experienced explosive growth and transformed the study of neural mechanisms across health and disease. However, given the diversity of sophisticated tools for handling neuroimaging data, the field faces challenges in method integration, particularly across multiple modalities and species. Specifically, researchers often have to rely on siloed approaches which limit reproducibility, with idiosyncratic data organization and limited software interoperability.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>To address these challenges, we have developed Quantitative Neuroimaging Environment &amp;amp; Toolbox (QuNex), a platform for consistent end-to-end processing and analytics. QuNex provides several novel functionalities for neuroimaging analyses, including a \u201cturnkey\u201d command for the reproducible deployment of custom workflows, from onboarding raw data to generating analytic features.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The platform enables interoperable integration of multi-modal, community-developed neuroimaging software through an extension framework with a software development kit (SDK) for seamless integration of community tools. Critically, it supports high-throughput, parallel processing in high-performance compute environments, either locally or in the cloud. Notably, QuNex has successfully processed over 10,000 scans across neuroimaging consortia, including multiple clinical datasets. Moreover, QuNex enables integration of human and non-human workflows\n                      <jats:italic>via<\/jats:italic>\n                      a cohesive translational platform.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>Collectively, this effort stands to significantly impact neuroimaging method integration across acquisition approaches, pipelines, datasets, computational environments, and species. Building on this platform will enable more rapid, scalable, and reproducible impact of neuroimaging technology across health and disease.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fninf.2023.1104508","type":"journal-article","created":{"date-parts":[[2023,4,5]],"date-time":"2023-04-05T01:05:01Z","timestamp":1680656701000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":40,"title":["QuNex\u2014An integrative platform for reproducible neuroimaging analytics"],"prefix":"10.3389","volume":"17","author":[{"given":"Jie Lisa","family":"Ji","sequence":"first","affiliation":[]},{"given":"Jure","family":"Dem\u0161ar","sequence":"additional","affiliation":[]},{"given":"Clara","family":"Fonteneau","sequence":"additional","affiliation":[]},{"given":"Zailyn","family":"Tamayo","sequence":"additional","affiliation":[]},{"given":"Lining","family":"Pan","sequence":"additional","affiliation":[]},{"given":"Aleksij","family":"Kralji\u010d","sequence":"additional","affiliation":[]},{"given":"Andra\u017e","family":"Matkovi\u010d","sequence":"additional","affiliation":[]},{"given":"Nina","family":"Purg","sequence":"additional","affiliation":[]},{"given":"Markus","family":"Helmer","sequence":"additional","affiliation":[]},{"given":"Shaun","family":"Warrington","sequence":"additional","affiliation":[]},{"given":"Anderson","family":"Winkler","sequence":"additional","affiliation":[]},{"given":"Valerio","family":"Zerbi","sequence":"additional","affiliation":[]},{"given":"Timothy S.","family":"Coalson","sequence":"additional","affiliation":[]},{"given":"Matthew F.","family":"Glasser","sequence":"additional","affiliation":[]},{"given":"Michael P.","family":"Harms","sequence":"additional","affiliation":[]},{"given":"Stamatios N.","family":"Sotiropoulos","sequence":"additional","affiliation":[]},{"given":"John D.","family":"Murray","sequence":"additional","affiliation":[]},{"given":"Alan","family":"Anticevic","sequence":"additional","affiliation":[]},{"given":"Grega","family":"Repov\u0161","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2023,4,5]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1016\/j.neuroimage.2017.10.034","article-title":"Image processing and quality control for the first 10,000 brain imaging datasets from UK biobank","volume":"166","author":"Alfaro-Almagro","year":"2018","journal-title":"Neuroimage"},{"key":"B2","doi-asserted-by":"publisher","first-page":"870","DOI":"10.1016\/S1053-8119(03)00336-7","article-title":"How to correct susceptibility distortions in spin-echo echo-planar images: application to diffusion tensor imaging","volume":"20","author":"Andersson","year":"2003","journal-title":"Neuroimage"},{"key":"B3","doi-asserted-by":"publisher","first-page":"1063","DOI":"10.1016\/j.neuroimage.2015.10.019","article-title":"An integrated approach to correction for off-resonance effects and subject movement in diffusion mr imaging","volume":"125","author":"Andersson","year":"2016","journal-title":"Neuroimage"},{"key":"B4","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1016\/j.neuroimage.2011.10.025","article-title":"SPM: a history","volume":"62","author":"Ashburner","year":"2012","journal-title":"Neuroimage"},{"key":"B5","doi-asserted-by":"publisher","first-page":"116800","DOI":"10.1016\/j.neuroimage.2020.116800","article-title":"Towards HCP-style macaque connectomes: 24-channel 3t multi-array coil, MRI sequences and preprocessing","volume":"215","author":"Autio","year":"2020","journal-title":"NeuroImage"},{"key":"B6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41597-019-0073-y","article-title":"The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services","volume":"6","author":"Avesani","year":"2019","journal-title":"Sci. Data"},{"key":"B7","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1016\/j.neuroimage.2013.05.033","article-title":"Function in the human connectome: task-fMRI and individual differences in behavior","volume":"80","author":"Barch","year":"2013","journal-title":"Neuroimage"},{"key":"B8","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1016\/j.neuroimage.2006.09.018","article-title":"Probabilistic diffusion tractography with multiple fibre orientations: what can we gain?","volume":"34","author":"Behrens","year":"2007","journal-title":"Neuroimage"},{"key":"B9","doi-asserted-by":"publisher","first-page":"2170","DOI":"10.1212\/WNL.0000000000002219","article-title":"The wernicke area: modern evidence and a reinterpretation","volume":"85","author":"Binder","year":"2015","journal-title":"Neurology"},{"key":"B10","doi-asserted-by":"publisher","first-page":"1465","DOI":"10.1016\/j.neuroimage.2010.09.048","article-title":"Mapping anterior temporal lobe language areas with fMRI: a multicenter normative study","volume":"54","author":"Binder","year":"2011","journal-title":"Neuroimage"},{"key":"B11","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1038\/s41586-020-2314-9","article-title":"Variability in the analysis of a single neuroimaging dataset by many teams","volume":"582","author":"Botvinik-Nezer","year":"2020","journal-title":"Nature"},{"key":"B12","doi-asserted-by":"publisher","first-page":"4207","DOI":"10.1523\/JNEUROSCI.16-13-04207.1996","article-title":"Linear systems analysis of functional magnetic resonance imaging in human v1","volume":"16","author":"Boynton","year":"1996","journal-title":"J. Neurosci"},{"key":"B13","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1038\/s41586-018-0579-z","article-title":"The uk biobank resource with deep phenotyping and genomic data","volume":"562","author":"Bycroft","year":"2018","journal-title":"Nature"},{"key":"B14","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/j.dcn.2018.03.001","article-title":"The adolescent brain cognitive development (ABCD) study: imaging acquisition across 21 sites","volume":"32","author":"Casey","year":"2018","journal-title":"Dev. Cogn. Neurosci"},{"key":"B15","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1038\/s41592-021-01185-5","article-title":"Qsiprep: an integrative platform for preprocessing and reconstructing diffusion MRI data","volume":"18","author":"Cieslak","year":"2021","journal-title":"Nat. Methods"},{"key":"B16","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1006\/cbmr.1996.0014","article-title":"AFNI: software for analysis and visualization of functional magnetic resonance neuroimages","volume":"29","author":"Cox","year":"1996","journal-title":"Comput. Biomed. Res"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2022.119612","article-title":"Micapipe: a pipeline for multimodal neuroimaging and connectome analysis","author":"Cruces","year":"2022","journal-title":"NeuroImage"},{"key":"B18","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1016\/j.cortex.2018.11.028","article-title":"Large-scale comparative neuroimaging: where are we and what do we need?","volume":"118","author":"de Schotten","year":"2019","journal-title":"Cortex"},{"key":"B19","doi-asserted-by":"publisher","first-page":"22","DOI":"10.3389\/neuro.11.022.2009","article-title":"Efficient, distributed and interactive neuroimaging data analysis using the loni pipeline","volume":"3","author":"Dinov","year":"2009","journal-title":"Front. Neuroinform"},{"key":"B20","doi-asserted-by":"publisher","first-page":"e53232","DOI":"10.7554\/eLife.53232","article-title":"Cross-species cortical alignment identifies different types of anatomical reorganization in the primate temporal lobe","volume":"9","author":"Eichert","year":"2020","journal-title":"Elife"},{"key":"B21","doi-asserted-by":"publisher","first-page":"118543","DOI":"10.1016\/j.neuroimage.2021.118543","article-title":"The human connectome project: a retrospective","volume":"2021","author":"Elam","year":"2021","journal-title":"NeuroImage"},{"key":"B22","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1038\/s41592-018-0235-4","article-title":"fmriprep: a robust preprocessing pipeline for functional MRI","volume":"16","author":"Esteban","year":"2019","journal-title":"Nat. Methods"},{"key":"B23","doi-asserted-by":"publisher","first-page":"448","DOI":"10.1111\/j.1749-6632.2009.04582.x","article-title":"Broca's area in language, action, and music","volume":"1169","author":"Fadiga","year":"2009","journal-title":"Ann. N. Y. Acad. Sci"},{"key":"B24","doi-asserted-by":"publisher","first-page":"3508","DOI":"10.1093\/cercor\/bhw157","article-title":"The human brainnetome atlas: a new brain atlas based on connectional architecture","volume":"26","author":"Fan","year":"2016","journal-title":"Cereb. Cortex"},{"key":"B25","doi-asserted-by":"publisher","first-page":"774","DOI":"10.1016\/j.neuroimage.2012.01.021","article-title":"Freesurfer","volume":"62","author":"Fischl","year":"2012","journal-title":"Neuroimage"},{"key":"B26","doi-asserted-by":"publisher","first-page":"11435","DOI":"10.1523\/JNEUROSCI.2388-08.2008","article-title":"Dissociating the human language pathways with high angular resolution diffusion fiber tractography","volume":"28","author":"Frey","year":"2008","journal-title":"J. Neurosci"},{"key":"B27","doi-asserted-by":"publisher","first-page":"1357","DOI":"10.1152\/physrev.00006.2011","article-title":"The brain basis of language processing: from structure to function","volume":"91","author":"Friederici","year":"2011","journal-title":"Physiol. Rev"},{"key":"B28","doi-asserted-by":"publisher","first-page":"2458","DOI":"10.1073\/pnas.0509389103","article-title":"The brain differentiates human and non-human grammars: functional localization and structural connectivity","volume":"103","author":"Friederici","year":"2006","journal-title":"Proc. Natl. Acad. Sci. U.S.A"},{"key":"B29","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1016\/j.conb.2012.10.002","article-title":"The language network","volume":"23","author":"Friederici","year":"2013","journal-title":"Curr. Opin. Neurobiol"},{"key":"B30","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1038\/nature18933","article-title":"A multi-modal parcellation of human cerebral cortex","volume":"536","author":"Glasser","year":"","journal-title":"Nature"},{"key":"B31","doi-asserted-by":"publisher","first-page":"1175","DOI":"10.1038\/nn.4361","article-title":"The human connectome project's neuroimaging approach","volume":"19","author":"Glasser","year":"","journal-title":"Nat. Neurosci"},{"key":"B32","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1016\/j.neuroimage.2013.04.127","article-title":"The minimal preprocessing pipelines for the human connectome project","volume":"80","author":"Glasser","year":"2013","journal-title":"Neuroimage"},{"key":"B33","doi-asserted-by":"publisher","first-page":"11597","DOI":"10.1523\/JNEUROSCI.2180-11.2011","article-title":"Mapping human cortical areas in vivo based on myelin content as revealed by t1-and t2-weighted MRI","volume":"31","author":"Glasser","year":"2011","journal-title":"J. Neurosci"},{"key":"B34","doi-asserted-by":"publisher","first-page":"748","DOI":"10.1016\/j.neuroimage.2012.01.083","article-title":"Brainvoyager-past, present, future","volume":"62","author":"Goebel","year":"2012","journal-title":"Neuroimage"},{"key":"B35","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/sdata.2016.44","article-title":"The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments","volume":"3","author":"Gorgolewski","year":"2016","journal-title":"Sci. Data"},{"key":"B36","doi-asserted-by":"publisher","first-page":"22","DOI":"10.3389\/fninf.2012.00022","article-title":"Open is not enough. let's take the next step: an integrated, community-driven computing platform for neuroscience","volume":"6","author":"Halchenko","year":"2012","journal-title":"Front. Neuroinform"},{"key":"B37","doi-asserted-by":"publisher","first-page":"117726","DOI":"10.1016\/j.neuroimage.2021.117726","article-title":"The nonhuman primate neuroimaging and neuroanatomy project","volume":"229","author":"Hayashi","year":"2021","journal-title":"Neuroimage"},{"key":"B38","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.1016\/j.neuroimage.2015.06.076","article-title":"Xnat central: Open sourcing imaging research data","volume":"124","author":"Herrick","year":"2016","journal-title":"NeuroImage"},{"key":"B39","doi-asserted-by":"publisher","first-page":"1846","DOI":"10.1002\/mrm.24204","article-title":"Model-based analysis of multishell diffusion MR data for tractography: how to get over fitting problems","volume":"68","author":"Jbabdi","year":"2012","journal-title":"Magn. Resonan. Med"},{"key":"B40","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1006\/nimg.2002.1132","article-title":"Improved optimization for the robust and accurate linear registration and motion correction of brain images","volume":"17","author":"Jenkinson","year":"2002","journal-title":"Neuroimage"},{"key":"B41","doi-asserted-by":"publisher","first-page":"4463","DOI":"10.1093\/cercor\/bhy306","article-title":"Schizophrenia exhibits bi-directional brain-wide alterations in cortico-striato-cerebellar circuits","volume":"29","author":"Ji","year":"","journal-title":"Cereb. Cortex"},{"key":"B42","doi-asserted-by":"publisher","first-page":"e66968","DOI":"10.7554\/eLife.66968.sa2","article-title":"Mapping brain-behavior space relationships along the psychosis spectrum","volume":"10","author":"Ji","year":"2021","journal-title":"Elife"},{"key":"B43","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/j.neuroimage.2018.10.006","article-title":"Mapping the human brain's cortical-subcortical functional network organization","volume":"185","author":"Ji","year":"","journal-title":"NeuroImage"},{"key":"B44","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1148\/rg.2020190112","article-title":"MRI techniques to decrease imaging times in children","volume":"40","author":"Kozak","year":"2020","journal-title":"Radiographics"},{"key":"B45","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1385\/NI:5:1:11","article-title":"The extensible neuroimaging archive toolkit","volume":"5","author":"Marcus","year":"2007","journal-title":"Neuroinformatics"},{"key":"B46","doi-asserted-by":"publisher","first-page":"654","DOI":"10.1038\/s41586-022-04492-9","article-title":"Reproducible brain-wide association studies require thousands of individuals","volume":"603","author":"Marek","year":"2022","journal-title":"Nature"},{"key":"B47","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1146\/annurev-neuro-100220-025942","article-title":"A common space approach to comparative neuroscience","volume":"44","author":"Mars","year":"2021","journal-title":"Annu. Rev. Neurosci"},{"key":"B48","doi-asserted-by":"publisher","first-page":"e35237","DOI":"10.7554\/eLife.35237","article-title":"Whole brain comparative anatomy using connectivity blueprints","volume":"7","author":"Mars","year":"2018","journal-title":"Elife"},{"key":"B49","doi-asserted-by":"publisher","first-page":"379","DOI":"10.3389\/fnins.2015.00379","article-title":"A comparison of freesurfer-generated data with and without manual intervention","volume":"9","author":"McCarthy","year":"2015","journal-title":"Front. Neurosci"},{"key":"B50","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/j.neuron.2018.08.039","article-title":"An open resource for non-human primate imaging","volume":"100","author":"Milham","year":"2018","journal-title":"Neuron"},{"key":"B51","doi-asserted-by":"publisher","first-page":"5","DOI":"10.3389\/fninf.2019.00005","article-title":"Funp (fusion of neuroimaging preprocessing) pipelines: a fully automated preprocessing software for functional magnetic resonance imaging","volume":"13","author":"Park","year":"2019","journal-title":"Front. Neuroinform"},{"key":"B52","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1016\/j.neuroimage.2012.03.017","article-title":"Steps toward optimizing motion artifact removal in functional connectivity MRI; a reply to carp","volume":"76","author":"Power","year":"2013","journal-title":"Neuroimage"},{"key":"B53","doi-asserted-by":"publisher","first-page":"1402","DOI":"10.1016\/j.neuroimage.2012.02.084","article-title":"Within-subject template estimation for unbiased longitudinal image analysis","volume":"61","author":"Reuter","year":"2012","journal-title":"Neuroimage"},{"key":"B54","doi-asserted-by":"publisher","first-page":"689675","DOI":"10.3389\/fninf.2021.689675","article-title":"Clinica: An open-source software platform for reproducible clinical neuroscience studies","volume":"15","author":"Routier","year":"2021","journal-title":"Front. Neuroinform"},{"key":"B55","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1016\/j.neuroimage.2013.11.046","article-title":"Automatic denoising of functional MRI data: combining independent component analysis and hierarchical fusion of classifiers","volume":"90","author":"Salimi-Khorshidi","year":"2014","journal-title":"Neuroimage"},{"key":"B56","doi-asserted-by":"publisher","first-page":"3095","DOI":"10.1093\/cercor\/bhx179","article-title":"Local-global parcellation of the human cerebral cortex from intrinsic functional connectivity MRI","volume":"28","author":"Schaefer","year":"2018","journal-title":"Cereb. Cortex"},{"key":"B57","doi-asserted-by":"publisher","first-page":"S208","DOI":"10.1016\/j.neuroimage.2004.07.051","article-title":"Advances in functional and structural mr image analysis and implementation as fsl","volume":"23","author":"Smith","year":"2004","journal-title":"Neuroimage"},{"key":"B58","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1016\/j.neuroimage.2008.03.061","article-title":"Threshold-free cluster enhancement: addressing problems of smoothing, threshold dependence and localisation in cluster inference","volume":"44","author":"Smith","year":"2009","journal-title":"Neuroimage"},{"key":"B59","doi-asserted-by":"publisher","first-page":"678403","DOI":"10.3389\/fninf.2021.678403","article-title":"Flywheeltools: data curation and manipulation on the flywheel platform","volume":"15","author":"Tapera","year":"2021","journal-title":"Front. Neuroinform"},{"key":"B60","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1016\/S0959-4388(02)00361-6","article-title":"Windows on the brain: the emerging role of atlases and databases in neuroscience","volume":"12","author":"Van Essen","year":"2002","journal-title":"Curr. Opin. Neurobiol"},{"key":"B61","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1016\/j.neuroimage.2013.05.041","article-title":"The wu-minn human connectome project: an overview","volume":"80","author":"Van Essen","year":"2013","journal-title":"Neuroimage"},{"key":"B62","doi-asserted-by":"publisher","first-page":"116923","DOI":"10.1016\/j.neuroimage.2020.116923","article-title":"Xtract - standardised protocols for automated tractography in the human and macaque brain","volume":"217","author":"Warrington","year":"2020","journal-title":"NeuroImage"},{"key":"B63","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1016\/j.neuroimage.2014.01.060","article-title":"Permutation inference for the general linear model","volume":"92","author":"Winkler","year":"2014","journal-title":"Neuroimage"},{"key":"B64","doi-asserted-by":"publisher","first-page":"1486","DOI":"10.1002\/hbm.23115","article-title":"Non-parametric combination and related permutation tests for neuroimaging","volume":"37","author":"Winkler","year":"2016","journal-title":"Hum. Brain Mapp"},{"key":"B65","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.neuroimage.2015.07.090","article-title":"Mapping the mouse brain with RS-fMRI: an optimized pipeline for functional network identification","volume":"123","author":"Zerbi","year":"2015","journal-title":"Neuroimage"}],"container-title":["Frontiers in Neuroinformatics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fninf.2023.1104508\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,5]],"date-time":"2023-04-05T01:05:04Z","timestamp":1680656704000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fninf.2023.1104508\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4,5]]},"references-count":65,"alternative-id":["10.3389\/fninf.2023.1104508"],"URL":"https:\/\/doi.org\/10.3389\/fninf.2023.1104508","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.06.03.494750","asserted-by":"object"}]},"ISSN":["1662-5196"],"issn-type":[{"value":"1662-5196","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,4,5]]},"article-number":"1104508"}}