Step 2
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. Go slow. Do not place the markers too fast (use 1 s for each)
- 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
- After placing the last mark (Trachea), watch temporary lung masks being created on the display
- Place additional markers or delete from present ones if needed
- If the temporary masks fit well, press "Apply" and produce permanent mask segmentations.
- In noisy or weak datasets you may want to adapt the volmetric threshold range (hidden in "Advanced").
If you get mask leakages please set the maximum value down to -400.
A good mask result looks like this:
