{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:14:10Z","timestamp":1760145250732,"version":"build-2065373602"},"reference-count":36,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2024,7,12]],"date-time":"2024-07-12T00:00:00Z","timestamp":1720742400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"RC 5 \u00d7 1000 2020\u20132021"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["JFMK"],"abstract":"<jats:p>We aim to develop a deep learning-based algorithm for automated segmentation of thigh muscles and subcutaneous adipose tissue (SAT) from T1-weighted muscle MRIs from patients affected by muscular dystrophies (MDs). From March 2019 to February 2022, adult and pediatric patients affected by MDs were enrolled from Azienda Ospedaliera Universitaria Pisana, Pisa, Italy (Institution 1) and the IRCCS Stella Maris Foundation, Calambrone-Pisa, Italy (Institution 2), respectively. All patients underwent a bilateral thighs MRI including an axial T1 weighted in- and out-of-phase (dual-echo). Both muscles and SAT were manually and separately segmented on out-of-phase image sets by a radiologist with 6 years of experience in musculoskeletal imaging. A U-Net1 and U-Net3 were built to automatically segment the SAT, all the thigh muscles together and the three muscular compartments separately. The dataset was randomly split into the on train, validation, and test set. The segmentation performance was assessed through the Dice similarity coefficient (DSC). The final cohort included 23 patients. The estimated DSC for U-Net1 was 96.8%, 95.3%, and 95.6% on train, validation, and test set, respectively, while the estimated accuracy for U-Net3 was 94.1%, 92.9%, and 93.9%. Both of the U-Nets achieved a median DSC of 0.95 for SAT segmentation. The U-Net1 and the U-Net3 achieved an optimal agreement with manual segmentation for the automatic segmentation. The so-developed neural networks have the potential to automatically segment thigh muscles and SAT in patients affected by MDs.<\/jats:p>","DOI":"10.3390\/jfmk9030123","type":"journal-article","created":{"date-parts":[[2024,7,12]],"date-time":"2024-07-12T11:28:03Z","timestamp":1720783683000},"page":"123","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Convolutional Neural Network-Based Automated Segmentation of Skeletal Muscle and Subcutaneous Adipose Tissue on Thigh MRI in Muscular Dystrophy Patients"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0842-5372","authenticated-orcid":false,"given":"Giacomo","family":"Aringhieri","sequence":"first","affiliation":[{"name":"Department of Translational Research and New Technology in Medicine and Surgery, Academic Radiology, University of Pisa, 56126 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8588-0323","authenticated-orcid":false,"given":"Guja","family":"Astrea","sequence":"additional","affiliation":[{"name":"Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56128 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniela","family":"Marfisi","sequence":"additional","affiliation":[{"name":"Institute of Clinical Physiology, National Research Council of Italy (IFC-CNR), 56124 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4003-3320","authenticated-orcid":false,"given":"Salvatore Claudio","family":"Fanni","sequence":"additional","affiliation":[{"name":"Department of Translational Research and New Technology in Medicine and Surgery, Academic Radiology, University of Pisa, 56126 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8930-3491","authenticated-orcid":false,"given":"Gemma","family":"Marinella","sequence":"additional","affiliation":[{"name":"Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56128 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rosa","family":"Pasquariello","sequence":"additional","affiliation":[{"name":"Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56128 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giulia","family":"Ricci","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesco","family":"Sansone","sequence":"additional","affiliation":[{"name":"Institute of Clinical Physiology, National Research Council of Italy (IFC-CNR), 56124 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martina","family":"Sperti","sequence":"additional","affiliation":[{"name":"Department of Neurology, Careggi University Hospital, University of Florence, 50134 Florence, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8335-5541","authenticated-orcid":false,"given":"Alessandro","family":"Tonacci","sequence":"additional","affiliation":[{"name":"Institute of Clinical Physiology, National Research Council of Italy (IFC-CNR), 56124 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesca","family":"Torri","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sabrina","family":"Mat\u00e0","sequence":"additional","affiliation":[{"name":"SOD Neurologia 1, Dipartimento Neuromuscolo-Scheletrico e Degli Organi di Senso, Azienda Ospedaliera Universitaria Careggi, 50134 Florence, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6142-2384","authenticated-orcid":false,"given":"Gabriele","family":"Siciliano","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7950-4559","authenticated-orcid":false,"given":"Emanuele","family":"Neri","sequence":"additional","affiliation":[{"name":"Department of Translational Research and New Technology in Medicine and Surgery, Academic Radiology, University of Pisa, 56126 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Filippo Maria","family":"Santorelli","sequence":"additional","affiliation":[{"name":"Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, 56128 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0837-7799","authenticated-orcid":false,"given":"Raffaele","family":"Conte","sequence":"additional","affiliation":[{"name":"Institute of Clinical Physiology, National Research Council of Italy (IFC-CNR), 56124 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,7,12]]},"reference":[{"key":"ref_1","unstructured":"Lovering, R.M., Porter, N.C., and Bloch, R.J. 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