Bone Analysis Module – Erosion (BAM-Erosion), for installation as a module in 3D Slicer. This module is designed to quantify cortical bone interruptions and erosions from high resolution peripheral quantitative computed tomography scans (HR-pQCT, Scanco Medical) of patients with rheumatoid arthritis. Software was written in Python (v. 3.6.7) using VTK (v. 9.0.1), ITK (v5.2.1), SimpleITK (v.2.0.2). After publication, updates can be downloaded at https://github.com/ManskeLab/Bone_Analysis_Modules. Instructions for installation are available in the ReadMe document. The installation includes modules for: File conversion from native Scanco image forms (AIMs and ISQs) to formats support by 3D Slicer, including MetaImage (MHA) and Neuroimaging Informatics Technology Initiative (NIfTI). The BAM module was tested on multiple operating systems (Mac OS Monterey, Windows 10, and Ubuntu 22.04 LTS) to ensure compatibility. Automated segmentation of periosteal bone surface (utilizes algorithm similar to Burghardt et al. 2010 Bone doi: 10.1016/j.bone.2010.05.034 ) Cortical interruption detection and measurement of underlying trabecular bone loss (utilizes algorithm similar to Peters et al. 2018 BMC Med Imaging doi: 10.1007/s00223-017-0264-5 ) Erosion volume quantification after operator-identified erosions with seed points (utilizes algorithm similar to Töpfer et al. 2014 Rheumatology doi: 10.1093/rheumatology/ket259 ). Image registration to track longitudinal changes in erosion volume using rigid-body registration.

Project funded by the Arthritis Society (Canada) STAR-18-0189.