{"doi":"10.1162/imag.a.932","title":"Automated segmentation of multiple sclerosis lesions, paramagnetic rims, and central vein sign on MRI provides reliable diagnostic biomarkers","abstract":"Multiple sclerosis (MS) is characterized by central nervous system lesions detectable via MRI. Existing diagnostic criteria incorporate presence of white matter lesions, but specificity can be improved using MS-specific imaging biomarkers, including paramagnetic rim lesions (PRLs) and central vein sign (CVS). However, manual segmentation of lesions, PRLs, and CVS is time-consuming and subjective. We propose a fully-automated joint segmentation method called Automated Lesion, PRL, and CVS Analysis (ALPaCA). We trained ALPaCA using subject-level cross-validation on 47 adults with MS and 50 adults with radiological MS mimics. ALPaCA uses a voxel-wise lesion segmentation method to propose a large set of lesion candidates. Lesion candidates are input into a multi-contrast, multi-label 3D convolutional neural network as 3D patches to produce lesion, PRL, and CVS predictions. When multiple lesions exist within a patch, an attention mechanism identifies which lesion candidate to classify. At the lesion level, ALPaCA achieves cross-validation areas under the receiver operating characteristic curve (AUROCs) of 0.95, 0.91, and 0.87 for lesion, PRL, and CVS classification, outperforming previous methods (all p < 0.001). Correlations between subject-level ALPaCA lesion and PRL scores with manual counts are higher than those of previous methods (p < 0.001; p = 0.03). Subject-level ALPaCA PRL and CVS scores are highly associated with MS in logistic regressions, when controlling for age and sex (p < 0.001). ALPaCA allows for fully-automated simultaneous segmentation of MS lesions, PRLs, and CVS using clinically-feasible scans. These segmentations outperform existing methods at the lesion and subject level.","journal":"Imaging Neuroscience","year":2025,"id":542370,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9587,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1265772,"name":"Zheng Ren","orcid":"0009-0006-2430-4625","position":1,"is_corresponding":false},{"id":782905,"name":"Luyun Chen","orcid":"0000-0001-6861-180X","position":2,"is_corresponding":false},{"id":524056,"name":"Alessandra M. Valcarcel","orcid":"0000-0002-0869-1948","position":3,"is_corresponding":false},{"id":103391,"name":"Jordan D. Dworkin","orcid":"0000-0002-5720-1298","position":4,"is_corresponding":false},{"id":1431445,"name":"Brian Renner","orcid":"0000-0003-3729-5255","position":5,"is_corresponding":false},{"id":903842,"name":"Lynn Daboul","orcid":"0000-0002-2158-3992","position":6,"is_corresponding":false},{"id":657307,"name":"Carly M. O’Donnell","orcid":"0000-0003-2730-6758","position":7,"is_corresponding":false},{"id":1431946,"name":"Elizabeth D. Verter","orcid":null,"position":8,"is_corresponding":false},{"id":1000461,"name":"Abigail R. Manning","orcid":"0000-0001-9221-5612","position":9,"is_corresponding":false},{"id":559429,"name":"Kelly Clark","orcid":"0000-0002-3583-0966","position":10,"is_corresponding":false},{"id":284713,"name":"Eunchan Bae","orcid":"0000-0003-2941-3717","position":11,"is_corresponding":false},{"id":1359176,"name":"C.W. Chen","orcid":"0000-0001-5145-4625","position":12,"is_corresponding":false},{"id":559427,"name":"Carolyn Lou","orcid":"0000-0002-7604-833X","position":13,"is_corresponding":false},{"id":230040,"name":"Theodore D. Satterthwaite","orcid":"0000-0001-7072-9399","position":14,"is_corresponding":false},{"id":230046,"name":"Haochang Shou","orcid":"0000-0002-3043-047X","position":15,"is_corresponding":false},{"id":286342,"name":"Michel Bilello","orcid":"0000-0001-6313-5437","position":16,"is_corresponding":false},{"id":307555,"name":"Kunio Nakamura","orcid":"0000-0002-7833-8138","position":17,"is_corresponding":false},{"id":277151,"name":"Amit Bar‐Or","orcid":"0000-0001-7179-0335","position":18,"is_corresponding":false},{"id":241645,"name":"Peter A. Calabresi","orcid":"0000-0002-7776-6472","position":19,"is_corresponding":false},{"id":405189,"name":"Léorah Freeman","orcid":"0000-0002-5696-1797","position":20,"is_corresponding":false},{"id":347730,"name":"Roland G. Henry","orcid":"0000-0002-8232-7562","position":21,"is_corresponding":false},{"id":281941,"name":"Erin E. Longbrake","orcid":"0000-0002-1179-3937","position":22,"is_corresponding":false},{"id":347731,"name":"Jiwon Oh","orcid":"0000-0001-5519-6088","position":23,"is_corresponding":false},{"id":484419,"name":"Matthew K. Schindler","orcid":"0000-0003-0157-5669","position":24,"is_corresponding":false},{"id":247676,"name":"Martina Absinta","orcid":"0000-0003-0276-383X","position":25,"is_corresponding":false},{"id":656459,"name":"Andrew Solomon","orcid":"0000-0003-1602-1554","position":26,"is_corresponding":false},{"id":347735,"name":"Nancy L. Sicotte","orcid":"0000-0002-5131-3352","position":27,"is_corresponding":false},{"id":302249,"name":"Daniel Ontaneda","orcid":"0000-0002-2838-9148","position":28,"is_corresponding":false},{"id":230800,"name":"Daniel S. Reich","orcid":"0000-0002-2628-4334","position":29,"is_corresponding":false},{"id":247663,"name":"Pascal Sati","orcid":"0000-0002-6763-0125","position":30,"is_corresponding":false},{"id":52271,"name":"Russell T. Shinohara","orcid":"0000-0001-8627-8203","position":31,"is_corresponding":false},{"id":6592,"name":"Fengling Hu","orcid":"0000-0003-1081-5038","position":0,"is_corresponding":true}],"reference_count":32,"raw_metadata":null,"created_at":"2026-07-19T02:52:55.809501Z","pmid":"41089191","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}