Methods

We recommend describing LungCTAnalyzer in a paper's method section like this:

Methods:

CT datasets were imported into 3D Slicer (1,2) and lung masks were automatically segmented by LungCTSegmenter (3) extension using 13 manually marked points. Three points were placed in axial and coronal views inside the right and the left lung, and one point in the trachea. The segmentation algorithm uses a grow-cut algorithm with an intensity region restricted to -3000 to -250 HU. All lung masks were verified visually and in a few cases (n=x), slight corrections were manually done by either using the "Scissors" (cut away a part of the mask) or "Fill Between Slices" (adding a missing part to the lung mask) tool in the of the segment editor. The 3D Slicer LungCTAnalyzer extension (3) was then used to quantify "emphysematous", "inflated", "infiltrated", and "collapsed" lung in milliliters. Additionally, intrapulmonary vessels were segmented and subtracted from the beforementioned lung segments. There was no / there was (decide how you did it) compensation for intrapulmonary bronchi.

References:

(1) Fedorov A, Beichel R, Kalpathy-Cramer J, Finet J, Fillion-Robin JC, Pujol S, Bauer C, Jennings D, Fennessy F, Sonka M, Buatti J, Aylward S, Miller JV, Pieper S, Kikinis R. 3D Slicer as an image computing platform for the Quantitative Imaging Network. Magn Reson Imaging. 2012 Nov;30(9):1323-41. doi: 10.1016/j.mri.2012.05.001. Epub 2012 Jul 6. PMID: 22770690; PMCID: PMC3466397.

(2) Slicer 4.13: https://download.slicer.org/bitstream/614aca0a342a877cb3c65630

(3) LungCTAnalyzer extension: https://github.com/rbumm/SlicerLungCTAnalyzer