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. 2021 May 6;11:9697. doi: 10.1038/s41598-021-89111-9

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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The pipeline to generate a patient report can be subdivided into the following steps: (1) image acquisition using the HR-pQCT scanner, (2) segmentation of the second MC in the volumes, (3) calculation of the vBMD using the segmentation masks. As the manual and the automatic pipeline only differ in the segmentation step, the automatic segmentation pipeline can be considered a drop-in replacement of the semi-automatic, time-intensive expert segmentation.