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Rudolf Bumm edited this page Dec 22, 2020 · 12 revisions

Run Lung CT Segmenter to create lung masks

Select the 'Lung CT Segmenter' extension. It can be found in 3D Slicer under the 'Chest Imaging Platform' category
Pick the input volume (required): Select a high resolution lung images series of the presently loaded DICOM CT data set

Press the "Start" button

Follow the instructions on the screen, the manual procedures are simple and straightforward
- Place three markers on the right lung, axial view (red slice)
- Place three markers on the right lung, coronal view
- Place three markers on the left lung axial view (red slice)
- Place three markers on the left lung, coronal view
- Place one marker on the trachea, axial view

Watch temporary lung masks being created on the display
Place additional markers if needed
If the temporary masks fit well, press 'Apply" and produce permanent mask segmentations.
In noisy or weak datasets you may want to adopt the volmetric threshold range (hidden in "Advanced"). If you get mask leakages please thst the maximum value down to -400.