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We developed an open-source quantitative report (QReport) that integrates validated 3D T2-FLAIR quantification methods with multi-centre MS and healthy reference models, and presents outputs in a structured graphical report to support contextualised interpretation of clinically relevant biomarkers.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>2516 cross-sectional 3D T2-FLAIR scans from people with MS (pwMS) and healthy controls (HC) were retrospectively collected from 14 centres within Magnetic Resonance Imaging in MS (MAGNIMS) and affiliated sites, as well as open-source datasets. Validated T2-FLAIR-based algorithms quantified total and regional lesion count (LC), lesion volume (LV), brain volume (BV), and brain age gap estimation (BrainAGE). Distributions in pwMS and HC were estimated using quantile regression. A QReport was designed to present biomarkers and reference models in graphical formats. Four neuroradiologists assessed agreement between QReport outputs and their visual assessment, and evaluated its usefulness, in 22 cases.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We analysed scans from 1723 HC (age, mean\u2009\u00b1\u2009SD: 54.5\u2009\u00b1\u200916.0; range: 18\u201375; F\/M: 949\/774) and 793 pwMS (age, mean\u2009\u00b1\u2009SD: 43.0\u2009\u00b1\u200911.1; range: 18\u201375; F\/M: 538\/255) across 14 centres. The QReport presents single-subject measures contextualised against the 95th, 50th, and 5th percentile distributions in pwMS and HC, and includes BrainAGE. In 94% of evaluations, QReport outputs demonstrated Moderate-to-Complete agreement with visual assessment and were rated as useful in 82%.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>We developed an MS QReport requiring only 3D T2-FLAIR, integrating validated quantification algorithms and incorporating BrainAGE within a clinically interpretable framework.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1007\/s00234-026-04060-2","type":"journal-article","created":{"date-parts":[[2026,6,6]],"date-time":"2026-06-06T07:51:07Z","timestamp":1780732267000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["An automated quantitative report for multiple sclerosis using only 3D T2-fluid-attenuated inversion recovery 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Prados received a Guarantors of Brain fellowship 2017-2020. G. Pontillo received research grants from ECTRIMS-MAGNIMS and ESNR. O. Goodkin is an employee of Bayer Plc. A. Rovira serves\/ed on scientific advisory boards for Novartis, Sanofi-Genzyme, SyntheticMR, TensorMedical, Roche, Biogen, and OLEA Medical, and has received speaker honoraria from Bayer, Sanofi- Genzyme, Merck-Serono, Teva Pharmaceutical Industries Ltd, Novartis, Roche, Bristol-Myers and Biogen. Ayodeji Ijishakin is a founder of Mecha Health. M.A. Foster has received speaker honoraria from Merck. J. Palace has received support for scientific meetings and honorariums for advisory work from Merck Serono, Novartis, Chugai, Alexion, Roche, Medimmune, Argenx, Vitaccess, UCB, Mitsubishi, Amplo, Janssen. Grants from Alexion, Argenx, Roche, Medimmune, Amplo biotechnology. Patent ref P37347WO and licence agreement Numares multimarker MS diagnostics Shares in AstraZeneca. Her group has been awarded an ECTRIMS fellowship and a Sumaira Foundation grant to start later this year. A Charcot fellow worked in Oxford 2019-2021. She acknowledges partial funding to the trust by Highly specialised services NHS England. She is on the medical advisory boards of the Sumaira Foundation and MOG project charities, is a member of the Guthy Jackon Foundation Charity and is on the Board of the European Charcot Foundation and the steering committee of MAGNIMS and the UK NHSE IVIG Committee and chairman of the NHSE neuroimmunology patient pathway and ECTRIMS Council member on the educational committee since June 2023. On the ABN advisory groups for MS and neuroinflammation. S. Messina received honoraria for lecturing and advisory board activity from UCB and Biogen, and travel grant from Roche and Merck. R. Cortese received speaker honoraria and travel support from Roche, Merck, Sanofi-Genzyme, Novartis and Janssen. She was awarded a MAGNIMS-ECTRIMS fellowship in 2019. EAH received honoraria for advisory board activity from Sanofi-Genzyme, and his department has received honoraria for lecturing from Biogen and Merck. L.T. Westlye is a shareholder and advisor of baba.vision. M.A. Rocca received consulting fees from Biogen, Bristol Myers Squibb, Eli Lilly, Janssen, Roche; and speaker honoraria from AstraZeneca, Biogen, Bristol Myers Squibb, Bromatech, Celgene, Genzyme, Horizon Therapeutics Italy, Merck Serono SpA, Novartis, Roche, Sanofi and Teva. She receives research support from the MS Society of Canada, the Italian Ministry of Health, the Italian Ministry of University and Research, and Fondazione Italiana Sclerosi Multipla. She is Associate Editor for Multiple Sclerosis and Related Disorders. M. Filippi is Editor-in-Chief of the Journal of Neurology, Associate Editor of Human Brain Mapping, Neurological Sciences, and Radiology; received compensation for consulting services from Alexion, Almirall, Biogen, Merck, Novartis, Roche, Sanofi; speaking activities from Bayer, Biogen, Celgene, Chiesi Italia SpA, Eli Lilly, Genzyme, Janssen, Merck-Serono, Neopharmed Gentili, Novartis, Novo Nordisk, Roche, Sanofi, Takeda, and TEVA; participation in Advisory Boards for Alexion, Biogen, Bristol-Myers Squibb, Merck, Novartis, Roche, Sanofi, Sanofi-Aventis, Sanofi-Genzyme, Takeda; scientific direction of educational events for Biogen, Merck, Roche, Celgene, Bristol- Myers Squibb, Lilly, Novartis, Sanofi-Genzyme; he receives research support from Biogen Idec, Merck-Serono, Novartis, Roche, the Italian Ministry of Health, the Italian Ministry of University and Research, and Fondazione Italiana Sclerosi Multipla. A.Toosy has received speaker honoraria from Merck, Biomedia, Sereno Symposia International Foundation, Bayer and At the Limits and meeting expenses from Merck, Biogen Idec and Novartis He was the UK PI for two clinical trials sponsored by MEDDAY pharmaceutical company (MD1003 in optic neuropathy [MS-ON -NCT02220244] and progressive MS [MS-SPI2 - NCT02936037]). He has been supported by recent grants from the MRC (MR\/S026088\/1), NIHR BRC (541\/CAP\/OC\/818837) and RoseTrees Trust (A1332 and PGL21\/10079). He is an associate editor for Frontiers in Neurology - Neuro-ophthalmology section and on the editorial board for Neurology and Multiple Sclerosis Journal. O. Ciccarelli is an NIHR Research Professor (RP-2017-08-ST2-004); acts as a consultant for Biogen, Merck, Novartis, Roche, and Teva; and has received research grant support from the MS Society of Great Britain and Northern Ireland, the NIHR UCLH Biomedical Research Centre, the Rosetree Trust, the National MS Society, and the NIHR-HTA. H. Pemberton is an employee of GE Healthcare. J.H. Cole is a scientific advisor to and shareholder in BrainKey and Claritas HealthTech PTE. F. Barkhof receives NIHR funding and is a steering committee and iDMC member for Biogen, Merck, Roche, EISAI. Consultant for Roche, Biogen, Merck, IXICO, Jansen, Combinostics. Research agreements with Novartis, Merck, Biogen, GE, Roche. Co-founder and shareholder of Queen Square Analytics LTD. The remaining authors report no competing interests.F. Prados received a Guarantors of Brain fellowship 2017-2020. G. Pontillo received research grants from ECTRIMS-MAGNIMS and ESNR. O. Goodkin is an employee of Bayer Plc. A. Rovira serves\/ed on scientific advisory boards for Novartis, Sanofi-Genzyme, SyntheticMR, TensorMedical, Roche, Biogen, and OLEA Medical, and has received speaker honoraria from Bayer, Sanofi- Genzyme, Merck-Serono, Teva Pharmaceutical Industries Ltd, Novartis, Roche, Bristol-Myers and Biogen. Ayodeji Ijishakin is a founder of Mecha Health. M.A. Foster has received speaker honoraria from Merck. J. Palace has received support for scientific meetings and honorariums for advisory work from Merck Serono, Novartis, Chugai, Alexion, Roche, Medimmune, Argenx, Vitaccess, UCB, Mitsubishi, Amplo, Janssen. Grants from Alexion, Argenx, Roche, Medimmune, Amplo biotechnology. Patent ref P37347WO and licence agreement Numares multimarker MS diagnostics Shares in AstraZeneca. Her group has been awarded an ECTRIMS fellowship and a Sumaira Foundation grant to start later this year. A Charcot fellow worked in Oxford 2019-2021. She acknowledges partial funding to the trust by Highly specialised services NHS England. She is on the medical advisory boards of the Sumaira Foundation and MOG project charities, is a member of the Guthy Jackon Foundation Charity and is on the Board of the European Charcot Foundation and the steering committee of MAGNIMS and the UK NHSE IVIG Committee and chairman of the NHSE neuroimmunology patient pathway and ECTRIMS Council member on the educational committee since June 2023. On the ABN advisory groups for MS and neuroinflammation. S. Messina received honoraria for lecturing and advisory board activity from UCB and Biogen, and travel grant from Roche and Merck. R. Cortese received speaker honoraria and travel support from Roche, Merck, Sanofi-Genzyme, Novartis and Janssen. She was awarded a MAGNIMS-ECTRIMS fellowship in 2019. EAH received honoraria for advisory board activity from Sanofi-Genzyme, and his department has received honoraria for lecturing from Biogen and Merck. L.T. Westlye is a shareholder and advisor of baba.vision. M.A. Rocca received consulting fees from Biogen, Bristol Myers Squibb, Eli Lilly, Janssen, Roche; and speaker honoraria from AstraZeneca, Biogen, Bristol Myers Squibb, Bromatech, Celgene, Genzyme, Horizon Therapeutics Italy, Merck Serono SpA, Novartis, Roche, Sanofi and Teva. She receives research support from the MS Society of Canada, the Italian Ministry of Health, the Italian Ministry of University and Research, and Fondazione Italiana Sclerosi Multipla. She is Associate Editor for Multiple Sclerosis and Related Disorders. M. Filippi is Editor-in-Chief of the Journal of Neurology, Associate Editor of Human Brain Mapping, Neurological Sciences, and Radiology; received compensation for consulting services from Alexion, Almirall, Biogen, Merck, Novartis, Roche, Sanofi; speaking activities from Bayer, Biogen, Celgene, Chiesi Italia SpA, Eli Lilly, Genzyme, Janssen, Merck-Serono, Neopharmed Gentili, Novartis, Novo Nordisk, Roche, Sanofi, Takeda, and TEVA; participation in Advisory Boards for Alexion, Biogen, Bristol-Myers Squibb, Merck, Novartis, Roche, Sanofi, Sanofi-Aventis, Sanofi-Genzyme, Takeda; scientific direction of educational events for Biogen, Merck, Roche, Celgene, Bristol- Myers Squibb, Lilly, Novartis, Sanofi-Genzyme; he receives research support from Biogen Idec, Merck-Serono, Novartis, Roche, the Italian Ministry of Health, the Italian Ministry of University and Research, and Fondazione Italiana Sclerosi Multipla. A.Toosy has received speaker honoraria from Merck, Biomedia, Sereno Symposia International Foundation, Bayer and At the Limits and meeting expenses from Merck, Biogen Idec and Novartis He was the UK PI for two clinical trials sponsored by MEDDAY pharmaceutical company (MD1003 in optic neuropathy [MS-ON -NCT02220244] and progressive MS [MS-SPI2 - NCT02936037]). He has been supported by recent grants from the MRC (MR\/S026088\/1), NIHR BRC (541\/CAP\/OC\/818837) and RoseTrees Trust (A1332 and PGL21\/10079). He is an associate editor for Frontiers in Neurology - Neuro-ophthalmology section and on the editorial board for Neurology and Multiple Sclerosis Journal. O. Ciccarelli is an NIHR Research Professor (RP-2017-08-ST2-004); acts as a consultant for Biogen, Merck, Novartis, Roche, and Teva; and has received research grant support from the MS Society of Great Britain and Northern Ireland, the NIHR UCLH Biomedical Research Centre, the Rosetree Trust, the National MS Society, and the NIHR-HTA. H. Pemberton is an employee of GE Healthcare. J.H. Cole is a scientific advisor to and shareholder in BrainKey and Claritas HealthTech PTE. F. Barkhof receives NIHR funding and is a steering committee and iDMC member for Biogen, Merck, Roche, EISAI. Consultant for Roche, Biogen, Merck, IXICO, Jansen, Combinostics. Research agreements with Novartis, Merck, Biogen, GE, Roche. Co-founder and shareholder of Queen Square Analytics LTD. The remaining authors report no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}