Automated Segmentation of Trunk Musculature with a Deep CNN Trained from Sparse Annotations in Radiation Therapy Patients with Metastatic Spine Disease
Authors: Hong Vy , Pieper Steve , James Joanna , Anderson Dennis E , Pinter Csaba , Chang Yi Shuen , Aslan Bulent , Kozono David , Doyle Patrick F , Caplan Sarah , Kang Heejoo , Balboni Tracy , Spektor Alexander , Huynh Mai Anh , Keko Mario , Kikinis Ron , Hackney David B , Alkalay Ron N 
Published: January 2025

AbstractPurposeGiven the high prevalence of vertebral fractures post-radiotherapy in patients with metastatic spine disease, accurate and rapid muscle segmentation could support efforts to quantify muscular changes due to disease or treatment and enable biomechanical modeling for assessments of vertebral loading to improve personalized evaluation of vertebral fracture risk. This study presents a deep-learning approach for segmenting the complete volume of the trunk muscles from clinical CT images trained using sparsely annotated data.Materials and Methodswe extracted 2,009 axial CT images at the midpoint of each vertebral level (T4 to L4) from clinical CT of 148 cancer patients. The key extensor and flexor muscles (up to 8 muscles per side) were manually contoured and labeled per image in the thoracic and lumbar regions. We first trained a 2D nnU-Net deep-learning model on these labels to segment key extensor and flexor muscles. Using these sparse annotations per spine, we trained the model to segment each muscle’s entire 3D volumeResultsThe proposed method achieved comparable performance to manual segmentations, as assessed by expert radiologists, with a mean Dice score above 0.769. Significantly, the model drastically reduced segmentation time, from 4.3-6.5 hours for manual segmentation of 14 single axial CT images to approximately 1 minute for segmenting the complete thoracic-abdominal 3D volume.ConclusionThe approach demonstrates high potential for automating 3D muscle segmentation, significantly reducing the manual intervention required for generating musculoskeletal models, and could be instrumental in enhancing clinical decision-making and patient care in radiation oncology.SummaryA deep learning 2D nnU-Net model, trained on a sparse set of 2D muscle annotations, successfully segmented the entire volume of 20 thoracolumbar muscles from cancer patients’ clinical CT data. The model showed a remarkable increase in segmentation efficacy and generalizability, achieving comparable performance to manual segmentations in delineating each muscle anatomy.Key Points▪ A deep learning model (2D nnU-Net), developed using a sparse set of single axial CT-slice at each mid-per vertebral level, containing manual image annotation of 20 thoracic and lumbar muscles, achieved comparable performance to manual segmentations, as assessed by expert radiologists, with a mean Dice score above 0.769.▪ The model drastically reduced segmentation time, from 4.3-6.5 hours for manual segmentation of 14 single axial CT images to approximately 1 minute for segmenting the complete thoracic-abdominal 3D volume.▪ Radiologist assessment based on a Likert scale (0-5) for clinical acceptability of the muscle anatomical segmentation showed strong model performance for a representative sample of clinical CT data (a (mean(SD) of 4.66 (0.73)) and external data (4.66 (0.73).