{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T05:05:36Z","timestamp":1789880736780,"version":"4.0.1"},"posted":{"date-parts":[[2026,9,8]]},"group-title":"Neuroscience","reference-count":58,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T00:00:00Z","timestamp":1788825600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"name":"NIH","award":["R01EB028259"],"award-info":[{"award-number":["R01EB028259"]}]},{"name":"NIH","award":["R01NS134694"],"award-info":[{"award-number":["R01NS134694"]}]},{"name":"NIH","award":["R00AG062230"],"award-info":[{"award-number":["R00AG062230"]}]},{"name":"NIH","award":["R21EB033516"],"award-info":[{"award-number":["R21EB033516"]}]},{"name":"NIH","award":["R00 AG080084"],"award-info":[{"award-number":["R00 AG080084"]}]},{"name":"NIH","award":["P41EB031771"],"award-info":[{"award-number":["P41EB031771"]}]},{"name":"DOD","award":["W81XWH2010819"],"award-info":[{"award-number":["W81XWH2010819"]}]},{"award":["[225924\/Z\/22\/Z]"],"award-info":[{"award-number":["[225924\/Z\/22\/Z]"]}],"id":[{"id":"https:\/\/ror.org\/029chgv08","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Purpose<\/jats:title>\n                  <jats:p>\n                    Magnetic resonance spectroscopic imaging (MRSI) is a versatile technique to investigate the spatial distribution of\n                    <jats:italic>in vivo<\/jats:italic>\n                    metabolism. However, processing MRSI data is demanding, and only a few software packages support end-to-end analysis. The goal of this study was to implement fully automated, end-to-end MRSI analysis into the open-source \u2018Osprey-MRSI\u2019 software package.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>\n                    MRSI-specific analysis and visualization capabilities were implemented, building on the existing Osprey workflow. Modifications included spatial transformation and filtering operations, automated brain masking and tissue segmentation of the MRSI data, improved lipid filtering, rapid integral maps, linear-combination modeling with explicit B\n                    <jats:sub>0<\/jats:sub>\n                    frequency-shift correction, and generation of quality-control maps and metabolic images. A fully interactive GUI and semi-interactive HTML reports provide a user-friendly way to inspect each step of the analysis. All analysis derivatives are also exported in NIfTI and NIfTI-MRS format for easy visualization and synergies with other toolboxes and modalities.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>\n                    The automated MRSI workflow was successfully used to analyze short- and medium-TE 3T\n                    <jats:italic>in vivo<\/jats:italic>\n                    MRSI datasets from all major vendors (Philips, GE, Siemens) across multiple sites. Correct coregistration of MRSI data and MR images was validated using phantom data from each vendor and existing MRSI processing tools.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>Osprey-MRSI offers state-of-the-art methods with minimal user interaction available for non-expert users. The modularity of the workflow and the modeling algorithm will foster innovation and development of novel MRSI-specific analysis methods.<\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.09.02.748934","type":"posted-content","created":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T21:40:11Z","timestamp":1788903611000},"source":"Crossref","is-referenced-by-count":0,"title":["Fully automated open-source analysis and interactive visualization of magnetic resonance spectroscopic imaging (MRSI) data in Osprey-MRSI"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7148-292X","authenticated-orcid":false,"given":"Helge J.","family":"Z\u00f6llner","sequence":"first","affiliation":[{"name":"Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2583-7571","authenticated-orcid":false,"given":"Alexander R.","family":"Craven","sequence":"additional","affiliation":[{"name":"Department of Clinical and Biological Psychology, University of Bergen, Bergen, Norway"},{"name":"Department of Clinical Engineering, Haukeland University Hospital, Bergen, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1285-1593","authenticated-orcid":false,"given":"Vasilis M.","family":"Karlaftis","sequence":"additional","affiliation":[{"name":"Oxford Centre for Integrative Neuroimaging (OxCIN), FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7159-7025","authenticated-orcid":false,"given":"William T.","family":"Clarke","sequence":"additional","affiliation":[{"name":"Oxford Centre for Integrative Neuroimaging (OxCIN), FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9104-134X","authenticated-orcid":false,"given":"Dillip K.","family":"Senapati","sequence":"additional","affiliation":[{"name":"Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6001-2383","authenticated-orcid":false,"given":"Doris D.M.","family":"Lin","sequence":"additional","affiliation":[{"name":"Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3083-9811","authenticated-orcid":false,"given":"Georg","family":"Oeltzschner","sequence":"additional","affiliation":[{"name":"Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6410-7793","authenticated-orcid":false,"given":"Peter B.","family":"Barker","sequence":"additional","affiliation":[{"name":"Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States"},{"name":"F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026091921450516000_2026.09.02.748934v2.1","doi-asserted-by":"publisher","DOI":"10.1002\/nbm.4309"},{"key":"2026091921450516000_2026.09.02.748934v2.2","doi-asserted-by":"publisher","DOI":"10.1002\/nbm.1025"},{"key":"2026091921450516000_2026.09.02.748934v2.3","doi-asserted-by":"publisher","DOI":"10.1101\/2023.08.31.23294888"},{"key":"2026091921450516000_2026.09.02.748934v2.4","doi-asserted-by":"publisher","DOI":"10.1002\/ima.22748"},{"key":"2026091921450516000_2026.09.02.748934v2.5","doi-asserted-by":"publisher","DOI":"10.1002\/nbm.5304"},{"key":"2026091921450516000_2026.09.02.748934v2.6","doi-asserted-by":"publisher","DOI":"10.1002\/mrm.28630"},{"key":"2026091921450516000_2026.09.02.748934v2.7","doi-asserted-by":"publisher","DOI":"10.1007\/s10334-026-01351-w"},{"key":"2026091921450516000_2026.09.02.748934v2.8","doi-asserted-by":"publisher","DOI":"10.1002\/nbm.4615"},{"key":"2026091921450516000_2026.09.02.748934v2.9","doi-asserted-by":"publisher","DOI":"10.1002\/mrm.22579"},{"key":"2026091921450516000_2026.09.02.748934v2.10","doi-asserted-by":"publisher","DOI":"10.21105\/joss.03646"},{"key":"2026091921450516000_2026.09.02.748934v2.11","doi-asserted-by":"publisher","DOI":"10.1101\/2020.02.17.949495"},{"key":"2026091921450516000_2026.09.02.748934v2.12","unstructured":"Truong P , Chow K , Cui L , et al. Automatic, Online Reconstruction of Advanced Single Voxel and Spec- troscopic Imaging Sequences. In: 34rd Annual Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM).; 2025."},{"key":"2026091921450516000_2026.09.02.748934v2.13","doi-asserted-by":"publisher","DOI":"10.3389\/fnimg.2025.1610658"},{"key":"2026091921450516000_2026.09.02.748934v2.14","doi-asserted-by":"publisher","DOI":"10.1088\/0957-0233\/20\/10\/104035"},{"key":"2026091921450516000_2026.09.02.748934v2.15","doi-asserted-by":"publisher","DOI":"10.1155\/2013\/169526"},{"key":"2026091921450516000_2026.09.02.748934v2.16","doi-asserted-by":"publisher","DOI":"10.1002\/nbm.4257"},{"key":"2026091921450516000_2026.09.02.748934v2.17","doi-asserted-by":"publisher","DOI":"10.1002\/mrm.29418"},{"key":"2026091921450516000_2026.09.02.748934v2.18","doi-asserted-by":"publisher","DOI":"10.1101\/2023.06.15.544935"},{"key":"2026091921450516000_2026.09.02.748934v2.19","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.5576035"},{"key":"2026091921450516000_2026.09.02.748934v2.20","doi-asserted-by":"publisher","DOI":"10.1002\/nbm.698"},{"key":"2026091921450516000_2026.09.02.748934v2.21","doi-asserted-by":"publisher","DOI":"10.1016\/j.jneumeth.2020.108827"},{"key":"2026091921450516000_2026.09.02.748934v2.22","doi-asserted-by":"publisher","DOI":"10.1002\/mrm.26091"},{"key":"2026091921450516000_2026.09.02.748934v2.23","doi-asserted-by":"publisher","DOI":"10.1016\/j.dcn.2024.101452"},{"key":"2026091921450516000_2026.09.02.748934v2.24","doi-asserted-by":"publisher","DOI":"10.1007\/s10916-023-01969-6"},{"key":"2026091921450516000_2026.09.02.748934v2.25","doi-asserted-by":"publisher","DOI":"10.1002\/mrm.30110"},{"key":"2026091921450516000_2026.09.02.748934v2.26","doi-asserted-by":"publisher","DOI":"10.17605\/OSF.IO\/VKDPR"},{"key":"2026091921450516000_2026.09.02.748934v2.27","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2019.116141"},{"key":"2026091921450516000_2026.09.02.748934v2.28","unstructured":"Friston K. Statistical Parametric Mapping: The Analysis of Functional Brain Images. Academic Press; 2007. http:\/\/books.google.com\/books?id=KZZcLqkxhFIC%5Cnpapers:\/\/8fdc0079-0571-40b9-b7fa-84608563a121\/Paper\/p10618."},{"key":"2026091921450516000_2026.09.02.748934v2.29","doi-asserted-by":"publisher","DOI":"10.1002\/mrm.25094"},{"key":"2026091921450516000_2026.09.02.748934v2.30","doi-asserted-by":"publisher","DOI":"10.1002\/nbm.4368"},{"key":"2026091921450516000_2026.09.02.748934v2.31","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmr.2017.04.004"},{"key":"2026091921450516000_2026.09.02.748934v2.32","doi-asserted-by":"publisher","DOI":"10.1002\/mrm.1910140104"},{"key":"2026091921450516000_2026.09.02.748934v2.33","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2364(87)90023-0"},{"key":"2026091921450516000_2026.09.02.748934v2.34","doi-asserted-by":"publisher","DOI":"10.1002\/mrm.30209"},{"key":"2026091921450516000_2026.09.02.748934v2.35","doi-asserted-by":"publisher","DOI":"10.1002\/mrm.27824"},{"key":"2026091921450516000_2026.09.02.748934v2.36","unstructured":"Lipid suppression in CSI with spatial priors and highly undersampled peripheral kD space - Bilgic - 2013 - Magnetic Resonance in Medicine - Wiley Online Library. https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/mrm.24399. Accessed March 13, 2026."},{"key":"2026091921450516000_2026.09.02.748934v2.37","unstructured":"Provencher S. LCModel & LCMgui User\u2019s Manual. LCModel & LCMgui User\u2019s Manual. http:\/\/sprovencher.com\/pub\/LCModel\/manual\/manual.pdf. Published 2020. Accessed April 28, 2020."},{"key":"2026091921450516000_2026.09.02.748934v2.38","doi-asserted-by":"publisher","DOI":"10.1002\/mrm.20901"},{"key":"2026091921450516000_2026.09.02.748934v2.39","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1522-2586(199904)9:4<531::AID-JMRI4>3.0.CO;2-L"},{"key":"2026091921450516000_2026.09.02.748934v2.40","doi-asserted-by":"publisher","DOI":"10.1002\/nbm.713"},{"key":"2026091921450516000_2026.09.02.748934v2.41","doi-asserted-by":"publisher","DOI":"10.1002\/mrm.27067"},{"key":"2026091921450516000_2026.09.02.748934v2.42","doi-asserted-by":"publisher","DOI":"10.1002\/jmri.23817"},{"key":"2026091921450516000_2026.09.02.748934v2.43","doi-asserted-by":"publisher","DOI":"10.1002\/jmri.22865"},{"key":"2026091921450516000_2026.09.02.748934v2.44","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2019.116189"},{"key":"2026091921450516000_2026.09.02.748934v2.45","doi-asserted-by":"crossref","unstructured":"Mori S , Wakana S , Zijl PCM van , Nagae-Poetscher LM . MRI Atlas of Human White Matter. 1. Aufl. s.l.: Elsevier professional; 2005.","DOI":"10.1016\/B978-044451741-8\/50001-9"},{"key":"2026091921450516000_2026.09.02.748934v2.46","doi-asserted-by":"publisher","DOI":"10.1016\/S0387-7604(99)00022-4"},{"key":"2026091921450516000_2026.09.02.748934v2.47","doi-asserted-by":"publisher","DOI":"10.1089\/neu.2012.2696"},{"key":"2026091921450516000_2026.09.02.748934v2.48","doi-asserted-by":"publisher","DOI":"10.1002\/nbm.2812"},{"key":"2026091921450516000_2026.09.02.748934v2.49","doi-asserted-by":"publisher","DOI":"10.1002\/nbm.1445"},{"key":"2026091921450516000_2026.09.02.748934v2.50","doi-asserted-by":"crossref","unstructured":"Das S , Zijdenbos A , Vins D , Harlap J , Evans A . LORIS: a web-based data management system for multi- center studies. Front Neuroinformatics. 2012;5. https:\/\/www.frontiersin.org\/articles\/10.3389\/fninf.2011.00037. Accessed January 26, 2023.","DOI":"10.3389\/fninf.2011.00037"},{"key":"2026091921450516000_2026.09.02.748934v2.51","doi-asserted-by":"publisher","DOI":"10.1148\/radiology.188.1.8511313"},{"key":"2026091921450516000_2026.09.02.748934v2.52","doi-asserted-by":"publisher","DOI":"10.1002\/nbm.4218"},{"key":"2026091921450516000_2026.09.02.748934v2.53","doi-asserted-by":"publisher","DOI":"10.1002\/mrm.29370"},{"key":"2026091921450516000_2026.09.02.748934v2.54","doi-asserted-by":"publisher","DOI":"10.1002\/mrm.22858"},{"key":"2026091921450516000_2026.09.02.748934v2.55","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuroimage.2024.120845"},{"key":"2026091921450516000_2026.09.02.748934v2.56","doi-asserted-by":"publisher","DOI":"10.1002\/nbm.70175"},{"key":"2026091921450516000_2026.09.02.748934v2.57","doi-asserted-by":"publisher","DOI":"10.3174\/ajnr.A9088"},{"key":"2026091921450516000_2026.09.02.748934v2.58","doi-asserted-by":"publisher","DOI":"10.58530\/2025\/4833"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.09.02.748934","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T04:45:27Z","timestamp":1789879527000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.09.02.748934"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,8]]},"references-count":58,"URL":"https:\/\/doi.org\/10.64898\/2026.09.02.748934","relation":{},"subject":[],"published":{"date-parts":[[2026,9,8]]},"subtype":"preprint"}}