Template Creation for High-Resolution Computed Tomography Scans of the Lung in R Software

Acad Radiol. 2020 Aug;27(8):e204-e215. doi: 10.1016/j.acra.2019.10.030. Epub 2019 Dec 13.


Rationale and objectives: A standard lung template could improve population-level analyses for computed tomography (CT) scans of the lung. We develop a fully automated preprocessing pipeline for image analysis of the lungs using updated methodologies and R software that results in the creation of a standard lung template. We apply this pipeline to CT scans from a sarcoidosis population, exploring the influence of registration on radiomic analyses.

Materials and methods: Using 65 high-resolution CT scans from healthy adults, we create a standard lung template by segmenting the left and right lungs, nonlinearly registering lung masks to an initial template mask, and using an unbiased, iterative procedure to converge to a standard lung shape (Dice similarity coefficient ≥0.99). We compare three-dimensional radiomic features between control and sarcoidosis patients, before and after registration to a study-specific lung template.

Results: The final lung template had a right lung volume of 2967 cm3 and left lung volume of 2623 cm3, with a median HU = -862. Registration significantly affected radiomic features, shifting the HU distribution to the left, decreasing variability, and increasing smoothness (p < 0.0001). The registration improved detective ability of radiomics; for contrast, autocorrelation, energy, and homogeneity, the group effect was significant postregistration (p < 0.05), but was not significant preregistration.

Conclusion: The final lung template and software used for its creation are publicly available via the lungct R package to facilitate its use in practice. This study advances lung imaging by developing tools to improve population-level analyses for various lung diseases.

Keywords: Atlas; Computed tomography; Lung; R Software; Template creation.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adult
  • Humans
  • Lung* / diagnostic imaging
  • Radionuclide Imaging
  • Software
  • Tomography, X-Ray Computed*