This 3D Slicer extension implements algorithms for semi-automated detection of cortical breaks and bone erosions in HR-pQCT images. Additional image analysis tools, such as automatic contouring and image registration are included as well.
These are the modules published in Bone: Zhao M, Tse JJ, Kuczynski MT, Brunet SC, Yan R, Engelke K, Peters M, van den Bergh J, van Rietbergen B, Stok KS, Barnabe C, Pauchard Y, Manske SL. Open-source image analysis tool for the identification and quantification of cortical interruptions and bone erosions in high-resolution peripheral quantitative computed tomography images of patients with rheumatoid arthritis. In Press. doi.org/10.1016/j.bone.2022.116571. While these modules may be updated over time, the original published version is available on Zenodo.
Install this Extension in 3D Slicer, or follow these steps to manually install:
- Get the latest version of the code.
cd to the directory where you want to download the code:
git clone https://github.com/ManskeLab/3DSlicer_Erosion_Analysis.gitTo update, cd to the directory where you downloaded the code and run git pull:
git pull- Install 3D Slicer.
- Open 3D Slicer and go to Edit > Application Settings > Modules.
- Expand the box "Additional module paths:" by clicking the arrow on the right side. This shows the “Add” and “Remove” buttons.
- Click “Add” and navigate to the directory where you downloaded the erosion analysis toolkits. Choose the directory of each toolkit separately i.e. AutomaticContour; ErosionVolume.
- After adding all the toolkits, click OK. Slicer wants to be restarted.
- After restarting Slicer, the toolkits should be listed in the “Bone” category under the "Modules:" list. An alternative way to access the toolkits is to click the magnifying glass beside the “Modules:” list and search for “Automatic Contour” or “Erosion Volume”.
Refer to wiki.