Step 2
Youtube video:
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
- If you want to use the last markups you have created with LungCTSegmenter consider just pressing the "l" (L key, small letter) shortcut on the keyboard. This creates the necessary "R", "L", and "T" markups instantly with the ones you have used during your last "Lung CT Segmenter" session.
- Otherwise: 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
- 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 volumetric threshold range (hidden in "Advanced").
If you get mask leakages please set the maximum value down to -400. Press "Update".
A good mask result looks like this:
