Hendrik Möller, Robert Graf, Joachim Schmitt, Benjamin Keinert, Hanna Schön, Matan Atad, Anjany Sekuboyina, Felix Streckenbach, Florian Kofler, Thomas Kroencke, Stefanie Bette, Stefan N Willich, Thomas Keil, Thoralf Niendorf, Tobias Pischon, Beate Endemann, Bjoern Menze, Daniel Rueckert, Jan S Kirschke
{"title":"SPINEPS--采用多类语义和实例分割的两阶段方法对 T2 加权磁共振图像进行全脊柱自动分割。","authors":"Hendrik Möller, Robert Graf, Joachim Schmitt, Benjamin Keinert, Hanna Schön, Matan Atad, Anjany Sekuboyina, Felix Streckenbach, Florian Kofler, Thomas Kroencke, Stefanie Bette, Stefan N Willich, Thomas Keil, Thoralf Niendorf, Tobias Pischon, Beate Endemann, Bjoern Menze, Daniel Rueckert, Jan S Kirschke","doi":"10.1007/s00330-024-11155-y","DOIUrl":null,"url":null,"abstract":"<p><strong>Objectives: </strong>Introducing SPINEPS, a deep learning method for semantic and instance segmentation of 14 spinal structures (ten vertebra substructures, intervertebral discs, spinal cord, spinal canal, and sacrum) in whole-body sagittal T2-weighted turbo spin echo images.</p><p><strong>Material and methods: </strong>This local ethics committee-approved study utilized a public dataset (train/test 179/39 subjects, 137 female), a German National Cohort (NAKO) subset (train/test 1412/65 subjects, mean age 53, 694 female), and an in-house dataset (test 10 subjects, mean age 70, 5 female). SPINEPS is a semantic segmentation model, followed by a sliding window approach utilizing a second model to create instance masks from the semantic ones. Segmentation evaluation metrics included the Dice score and average symmetrical surface distance (ASSD). Statistical significance was assessed using the Wilcoxon signed-rank test.</p><p><strong>Results: </strong>On the public dataset, SPINEPS outperformed a nnUNet baseline on every structure and metric (e.g., an average over vertebra instances: dice 0.933 vs 0.911, p < 0.001, ASSD 0.21 vs 0.435, p < 0.001). SPINEPS trained on automated annotations of the NAKO achieves an average global Dice score of 0.918 on the combined NAKO and in-house test split. Adding the training data from the public dataset outperforms this (average instance-wise Dice score over the vertebra substructures 0.803 vs 0.778, average global Dice score 0.931 vs 0.918).</p><p><strong>Conclusion: </strong>SPINEPS offers segmentation of 14 spinal structures in T2w sagittal images. It provides a semantic mask and an instance mask separating the vertebrae and intervertebral discs. This is the first publicly available algorithm to enable this segmentation.</p><p><strong>Key points: </strong>Question No publicly available automatic approach can yield semantic and instance segmentation masks for the whole spine (including posterior elements) in T2-weighted sagittal TSE images. Findings Segmenting semantically first and then instance-wise outperforms a baseline trained directly on instance segmentation. The developed model produces high-resolution MRI segmentations for the whole spine. Clinical relevance This study introduces an automatic approach to whole spine segmentation, including posterior elements, in arbitrary fields of view T2w sagittal MR images, enabling easy biomarker extraction, automatic localization of pathologies and degenerative diseases, and quantifying analyses as downstream research.</p>","PeriodicalId":12076,"journal":{"name":"European Radiology","volume":" ","pages":"1178-1189"},"PeriodicalIF":4.7000,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11836161/pdf/","citationCount":"0","resultStr":"{\"title\":\"SPINEPS-automatic whole spine segmentation of T2-weighted MR images using a two-phase approach to multi-class semantic and instance segmentation.\",\"authors\":\"Hendrik Möller, Robert Graf, Joachim Schmitt, Benjamin Keinert, Hanna Schön, Matan Atad, Anjany Sekuboyina, Felix Streckenbach, Florian Kofler, Thomas Kroencke, Stefanie Bette, Stefan N Willich, Thomas Keil, Thoralf Niendorf, Tobias Pischon, Beate Endemann, Bjoern Menze, Daniel Rueckert, Jan S Kirschke\",\"doi\":\"10.1007/s00330-024-11155-y\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Objectives: </strong>Introducing SPINEPS, a deep learning method for semantic and instance segmentation of 14 spinal structures (ten vertebra substructures, intervertebral discs, spinal cord, spinal canal, and sacrum) in whole-body sagittal T2-weighted turbo spin echo images.</p><p><strong>Material and methods: </strong>This local ethics committee-approved study utilized a public dataset (train/test 179/39 subjects, 137 female), a German National Cohort (NAKO) subset (train/test 1412/65 subjects, mean age 53, 694 female), and an in-house dataset (test 10 subjects, mean age 70, 5 female). SPINEPS is a semantic segmentation model, followed by a sliding window approach utilizing a second model to create instance masks from the semantic ones. Segmentation evaluation metrics included the Dice score and average symmetrical surface distance (ASSD). Statistical significance was assessed using the Wilcoxon signed-rank test.</p><p><strong>Results: </strong>On the public dataset, SPINEPS outperformed a nnUNet baseline on every structure and metric (e.g., an average over vertebra instances: dice 0.933 vs 0.911, p < 0.001, ASSD 0.21 vs 0.435, p < 0.001). SPINEPS trained on automated annotations of the NAKO achieves an average global Dice score of 0.918 on the combined NAKO and in-house test split. Adding the training data from the public dataset outperforms this (average instance-wise Dice score over the vertebra substructures 0.803 vs 0.778, average global Dice score 0.931 vs 0.918).</p><p><strong>Conclusion: </strong>SPINEPS offers segmentation of 14 spinal structures in T2w sagittal images. It provides a semantic mask and an instance mask separating the vertebrae and intervertebral discs. This is the first publicly available algorithm to enable this segmentation.</p><p><strong>Key points: </strong>Question No publicly available automatic approach can yield semantic and instance segmentation masks for the whole spine (including posterior elements) in T2-weighted sagittal TSE images. Findings Segmenting semantically first and then instance-wise outperforms a baseline trained directly on instance segmentation. The developed model produces high-resolution MRI segmentations for the whole spine. 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SPINEPS-automatic whole spine segmentation of T2-weighted MR images using a two-phase approach to multi-class semantic and instance segmentation.
Objectives: Introducing SPINEPS, a deep learning method for semantic and instance segmentation of 14 spinal structures (ten vertebra substructures, intervertebral discs, spinal cord, spinal canal, and sacrum) in whole-body sagittal T2-weighted turbo spin echo images.
Material and methods: This local ethics committee-approved study utilized a public dataset (train/test 179/39 subjects, 137 female), a German National Cohort (NAKO) subset (train/test 1412/65 subjects, mean age 53, 694 female), and an in-house dataset (test 10 subjects, mean age 70, 5 female). SPINEPS is a semantic segmentation model, followed by a sliding window approach utilizing a second model to create instance masks from the semantic ones. Segmentation evaluation metrics included the Dice score and average symmetrical surface distance (ASSD). Statistical significance was assessed using the Wilcoxon signed-rank test.
Results: On the public dataset, SPINEPS outperformed a nnUNet baseline on every structure and metric (e.g., an average over vertebra instances: dice 0.933 vs 0.911, p < 0.001, ASSD 0.21 vs 0.435, p < 0.001). SPINEPS trained on automated annotations of the NAKO achieves an average global Dice score of 0.918 on the combined NAKO and in-house test split. Adding the training data from the public dataset outperforms this (average instance-wise Dice score over the vertebra substructures 0.803 vs 0.778, average global Dice score 0.931 vs 0.918).
Conclusion: SPINEPS offers segmentation of 14 spinal structures in T2w sagittal images. It provides a semantic mask and an instance mask separating the vertebrae and intervertebral discs. This is the first publicly available algorithm to enable this segmentation.
Key points: Question No publicly available automatic approach can yield semantic and instance segmentation masks for the whole spine (including posterior elements) in T2-weighted sagittal TSE images. Findings Segmenting semantically first and then instance-wise outperforms a baseline trained directly on instance segmentation. The developed model produces high-resolution MRI segmentations for the whole spine. Clinical relevance This study introduces an automatic approach to whole spine segmentation, including posterior elements, in arbitrary fields of view T2w sagittal MR images, enabling easy biomarker extraction, automatic localization of pathologies and degenerative diseases, and quantifying analyses as downstream research.
期刊介绍:
European Radiology (ER) continuously updates scientific knowledge in radiology by publication of strong original articles and state-of-the-art reviews written by leading radiologists. A well balanced combination of review articles, original papers, short communications from European radiological congresses and information on society matters makes ER an indispensable source for current information in this field.
This is the Journal of the European Society of Radiology, and the official journal of a number of societies.
From 2004-2008 supplements to European Radiology were published under its companion, European Radiology Supplements, ISSN 1613-3749.