{"id":"https://openalex.org/W4412444952","doi":"https://doi.org/10.1109/tmi.2025.3588831","title":"Attention-Based Shape-Deformation Networks for Artifact-Free Geometry Reconstruction of Lumbar Spine From MR Images","display_name":"Attention-Based Shape-Deformation Networks for Artifact-Free Geometry Reconstruction of Lumbar Spine From MR Images","publication_year":2025,"publication_date":"2025-07-15","ids":{"openalex":"https://openalex.org/W4412444952","doi":"https://doi.org/10.1109/tmi.2025.3588831","pmid":"https://pubmed.ncbi.nlm.nih.gov/40663683"},"language":"en","primary_location":{"id":"doi:10.1109/tmi.2025.3588831","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tmi.2025.3588831","pdf_url":null,"source":{"id":"https://openalex.org/S58069681","display_name":"IEEE Transactions on Medical Imaging","issn_l":"0278-0062","issn":["0278-0062","1558-254X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Medical Imaging","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046293249","display_name":"Linchen Qian","orcid":null},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Linchen Qian","raw_affiliation_strings":["Department of Computer Science, University of Miami, Coral Gables, FL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Miami, Coral Gables, FL, USA","institution_ids":["https://openalex.org/I145608581"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115593303","display_name":"Jiasong Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiasong Chen","raw_affiliation_strings":["Department of Computer Science, University of Miami, Coral Gables, FL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Miami, Coral Gables, FL, USA","institution_ids":["https://openalex.org/I145608581"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070629109","display_name":"Linhai Ma","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Linhai Ma","raw_affiliation_strings":["Department of Emergency Medicine, Yale University School of Medicine, New Haven, CT, USA","Department of Emergency Medicine, Yale University School of medicine, 333 Cedar St, New Haven, CT, USA"],"affiliations":[{"raw_affiliation_string":"Department of Emergency Medicine, Yale University School of Medicine, New Haven, CT, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Emergency Medicine, Yale University School of medicine, 333 Cedar St, New Haven, CT, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015975510","display_name":"Timur Urakov","orcid":null},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]},{"id":"https://openalex.org/I4210157890","display_name":"Neurological Surgery","ror":"https://ror.org/04r0gp612","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210157890"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Timur Urakov","raw_affiliation_strings":["Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, USA","institution_ids":["https://openalex.org/I145608581","https://openalex.org/I4210157890"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004156323","display_name":"Weiyong Gu","orcid":null},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Weiyong Gu","raw_affiliation_strings":["Department of Mechanical and Aerospace Engineering, University of Miami, Coral Gables, FL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Mechanical and Aerospace Engineering, University of Miami, Coral Gables, FL, USA","institution_ids":["https://openalex.org/I145608581"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100426911","display_name":"Liang Liang","orcid":"https://orcid.org/0000-0001-7215-8577"},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liang Liang","raw_affiliation_strings":["Department of Computer Science, University of Miami, Coral Gables, FL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Miami, Coral Gables, FL, USA","institution_ids":["https://openalex.org/I145608581"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5046293249"],"corresponding_institution_ids":["https://openalex.org/I145608581"],"apc_list":null,"apc_paid":null,"fwci":0.6751,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.70831629,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"44","issue":"12","first_page":"5258","last_page":"5277"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T14510","display_name":"Medical Imaging and Analysis","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T14510","display_name":"Medical Imaging and Analysis","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10238","display_name":"Spine and Intervertebral Disc Pathology","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/2734","display_name":"Pathology and Forensic Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10776","display_name":"Spinal Fractures and Fixation Techniques","score":0.9740999937057495,"subfield":{"id":"https://openalex.org/subfields/2746","display_name":"Surgery"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.6050339937210083},{"id":"https://openalex.org/keywords/deformation","display_name":"Deformation (meteorology)","score":0.5876836180686951},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5833985209465027},{"id":"https://openalex.org/keywords/iterative-reconstruction","display_name":"Iterative reconstruction","score":0.5770753026008606},{"id":"https://openalex.org/keywords/artifact","display_name":"Artifact (error)","score":0.559924840927124},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4634428322315216},{"id":"https://openalex.org/keywords/lumbar-spine","display_name":"Lumbar spine","score":0.450702428817749},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.4385080933570862},{"id":"https://openalex.org/keywords/geology","display_name":"Geology","score":0.20486676692962646},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19733884930610657},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.17718574404716492}],"concepts":[{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.6050339937210083},{"id":"https://openalex.org/C204366326","wikidata":"https://www.wikidata.org/wiki/Q3027650","display_name":"Deformation (meteorology)","level":2,"score":0.5876836180686951},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5833985209465027},{"id":"https://openalex.org/C141379421","wikidata":"https://www.wikidata.org/wiki/Q6094427","display_name":"Iterative reconstruction","level":2,"score":0.5770753026008606},{"id":"https://openalex.org/C2779010991","wikidata":"https://www.wikidata.org/wiki/Q2720909","display_name":"Artifact (error)","level":2,"score":0.559924840927124},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4634428322315216},{"id":"https://openalex.org/C3017433307","wikidata":"https://www.wikidata.org/wiki/Q405478","display_name":"Lumbar spine","level":2,"score":0.450702428817749},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.4385080933570862},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.20486676692962646},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19733884930610657},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.17718574404716492},{"id":"https://openalex.org/C111368507","wikidata":"https://www.wikidata.org/wiki/Q43518","display_name":"Oceanography","level":1,"score":0.0},{"id":"https://openalex.org/C141071460","wikidata":"https://www.wikidata.org/wiki/Q40821","display_name":"Surgery","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D008159","descriptor_name":"Lumbar Vertebrae","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D008159","descriptor_name":"Lumbar Vertebrae","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D008159","descriptor_name":"Lumbar Vertebrae","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":true},{"descriptor_ui":"D008279","descriptor_name":"Magnetic Resonance Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D008279","descriptor_name":"Magnetic Resonance Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D008279","descriptor_name":"Magnetic Resonance Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055959","descriptor_name":"Intervertebral Disc Degeneration","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D055959","descriptor_name":"Intervertebral Disc Degeneration","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D055959","descriptor_name":"Intervertebral Disc Degeneration","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tmi.2025.3588831","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tmi.2025.3588831","pdf_url":null,"source":{"id":"https://openalex.org/S58069681","display_name":"IEEE Transactions on Medical Imaging","issn_l":"0278-0062","issn":["0278-0062","1558-254X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Medical Imaging","raw_type":"journal-article"},{"id":"pmid:40663683","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40663683","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE transactions on medical imaging","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Sustainable cities and communities","score":0.5,"id":"https://metadata.un.org/sdg/11"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1966188170","https://openalex.org/W2000121022","https://openalex.org/W2014745447","https://openalex.org/W2048388771","https://openalex.org/W2058822180","https://openalex.org/W2098979973","https://openalex.org/W2101689475","https://openalex.org/W2152826865","https://openalex.org/W2164777277","https://openalex.org/W2531335066","https://openalex.org/W2588744776","https://openalex.org/W2592929672","https://openalex.org/W2770937706","https://openalex.org/W2907492528","https://openalex.org/W2922479016","https://openalex.org/W2928133111","https://openalex.org/W2996290406","https://openalex.org/W3010721913","https://openalex.org/W3082275768","https://openalex.org/W3087644100","https://openalex.org/W3088477271","https://openalex.org/W3127751679","https://openalex.org/W3130872505","https://openalex.org/W3138516171","https://openalex.org/W3197957534","https://openalex.org/W3203480968","https://openalex.org/W3204614423","https://openalex.org/W3210067958","https://openalex.org/W4200586254","https://openalex.org/W4211092599","https://openalex.org/W4212875960","https://openalex.org/W4220801508","https://openalex.org/W4221163766","https://openalex.org/W4291301110","https://openalex.org/W4295934721","https://openalex.org/W4296351727","https://openalex.org/W4302009288","https://openalex.org/W4313372020","https://openalex.org/W4321232185","https://openalex.org/W4362603432","https://openalex.org/W4383903543"],"related_works":["https://openalex.org/W52840052","https://openalex.org/W3162837891","https://openalex.org/W1687852313","https://openalex.org/W3029243869","https://openalex.org/W2502336004","https://openalex.org/W1741504538","https://openalex.org/W4308623176","https://openalex.org/W4230676417","https://openalex.org/W2019696434","https://openalex.org/W2358078963"],"abstract_inverted_index":{"Lumbar":[0],"disc":[1],"degeneration,":[2],"a":[3,23,52,106,120,141,175],"progressive":[4],"structural":[5],"wear":[6],"and":[7,78,97,102,129,165],"tear":[8],"of":[9,40,89,108,137,168,174],"lumbar":[10,29,46,91,149],"intervertebral":[11],"disc,":[12],"is":[13,180],"regarded":[14],"as":[15],"an":[16,153],"essential":[17],"role":[18],"on":[19,140],"low":[20],"back":[21],"pain,":[22],"significant":[24],"global":[25],"health":[26],"concern.":[27],"Automated":[28],"spine":[30,92,150],"geometry":[31,88,151,163],"reconstruction":[32],"from":[33],"MR":[34],"images":[35],"will":[36],"enable":[37],"fast":[38],"measurement":[39],"medical":[41,69],"parameters":[42],"to":[43,50,133],"evaluate":[44],"the":[45,87,90,135,138,148,166,172],"status,":[47],"in":[48,152],"order":[49],"determine":[51],"suitable":[53],"treatment.":[54],"Existing":[55],"image":[56,127],"segmentation-based":[57],"techniques":[58],"often":[59],"generate":[60,161],"erroneous":[61],"segments":[62],"or":[63],"unstructured":[64],"point":[65],"clouds,":[66],"unsuitable":[67],"for":[68,110],"parameter":[70],"measurement.":[71],"In":[72],"this":[73],"work,":[74],"we":[75,103,114],"present":[76,105],"UNet-DeformSA":[77],"TransDeformer:":[79],"novel":[80],"attention-based":[81],"deep":[82],"neural":[83],"networks":[84,160],"that":[85,158],"reconstruct":[86],"with":[93,119],"high":[94],"spatial":[95],"accuracy":[96],"mesh":[98],"correspondence":[99],"across":[100],"patients,":[101],"also":[104],"variant":[107,167],"TransDeformer":[109,169],"error":[111],"estimation.":[112],"Specially,":[113],"devise":[115],"new":[116,121],"attention":[117,122],"modules":[118],"formula,":[123],"which":[124],"integrate":[125],"tokenized":[126,130],"features":[128,132],"shape":[131,142],"predict":[134,171],"displacements":[136],"points":[139],"template.":[143],"The":[144],"deformed":[145],"template":[146],"reveals":[147],"image.":[154],"Experiment":[155],"results":[156],"show":[157],"our":[159],"artifact-free":[162],"outputs,":[164],"can":[170],"errors":[173],"reconstructed":[176],"geometry.":[177],"Our":[178],"code":[179],"available":[181],"at":[182],"https://github.com/linchenq/TransDeformer-Mesh.":[183]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
