Automatic contouring

The automatic contouring algorithm generates the periosteal mask of the bone based on the gray value image.

Function¶

To use automatic contouring, use the following commands:

from ormir_xct.core.segmentation.autocontour import autocontour

autocontour(img, 
    mu_water, 
    rescale_slope, 
    rescale_intercept)

Input settings¶

HR-pQCT

PCD-CT

µCT

img: SITK image or path to image
mu_water: Linear attenuation coefficient of water. Default = 0.2409
rescale_slope: Slope used to rescale to BMD. Default = 1603.51904
rescale_intercept Intercept used to rescale to BMD. Default = -391.209015

Further information about the function and its inputs can be found here (link to the API coming soon!)

Examples and workflows¶

HR-pQCT

PCD-CT

µCT

Examples of how to use the function for the automatic contouring can be found in:

Workflows that include automatic contouring:

Automatic contouring workflow

Citation¶

HR-pQCT

PCD-CT

µCT

If you use this function, please cite it like this:

We used the method by Buie et al. (2007) and implemented in ORMIR-XCT (Kuczynski et al. (2024)).

References¶

Buie, H. R., Campbell, G. M., Klinck, R. J., MacNeil, J. A., & Boyd, S. K. (2007). Automatic segmentation of cortical and trabecular compartments based on a dual threshold technique for in vivo micro-CT bone analysis. Bone, 41(4), 505–515. 10.1016/j.bone.2007.07.007
Kuczynski, M. T., Neeteson, N. J., Stok, K. S., Burghardt, A. J., Hernandez, M. A. E., Vicory, J., Tse, J. J., Durongbhan, P., Bonaretti, S., Wong, A. K. O., Boyd, S. K., & Manske, S. L. (2024). ORMIR_XCT: A Python package for high resolution peripheral quantitative computed tomography image processing. Journal of Open Source Software, 9(97), 6084. 10.21105/joss.06084