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How to perform and correct lobe Segmentations

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Tom Doel edited this page Jan 25, 2021 · 1 revision

The automated lobe segmentation is based on the method published here:

  • Doel et al, Pulmonary lobe segmentation from CT images using fissureness, airways, vessels and multilevel B-splines (2012)

The algorith is fully automated; however there are certain steps which, may produce inaccurate results depending on your datasets. To fix this, there are manual verification and correction tools which you can perform at each step. With some help from the manual correction tools you can usually produce good lobe segmentations for most datasets.

The steps of the method are as follows:

  1. Segment the airways - SEGMENT REGION/Airways button on the gui (plugin code: PTKAirways.m)
  • to visualise the results of the airway segmentaiton step, click Airways on the GUI. The BLUE voxels are the segmented airways.
  1. Label the airways according to which pulmonary segment they serve - SEGMENT REGION/Lobal bronchi (plugin code: PTKAirwaysLabelledByLobe)
  • To visualise the results of airway labelling, click Lobar Bronchi on the GUI. The segmented airways are coloured by broncus.
  • WARNING: the automatic airway labelling algorithm is not completely robust. It may incorrectly label some of the airways, which will lead to errors in the final lobe segmentation. Hence the following inspection and correct step is required to ensure correct lobr segmentation
  1. MANUAL STEP: inspect the airway labelling and correct if necessary

  • Visualise the airway labelling by selecting Lobar Bronchi on the GUI. Each bronchus is assigned a label (colour) coloured according to the lobe it serves.

    • Blue (RIGHT UPPER LOBE)
    • Green (RIGHT MIDDLE LOBE)
    • Cyan (RIGHT LOWER LOBE)
    • Magenta (LEFT UPPER LOBE)
    • Yellow (LEFT LOWER LOBE)
    • Red - the algorithm is uncertain (you can assign a lobe to improve results)
    • Grey - the airway serves more than one lobe

  • If any bronchus is incorrectly coloured, you will need to modify the labels

    • Select the Correct tab to edit the labels
    • Find an incorrectly labelled airway, right-click and choose the correct label
    • When you change the label on a bronchus, the child bronchi will automatically be assigned that same label

  1. Segment the left and right lungs - SEGMENT REGION/Lungs button on the gui (plugin code: PTKLeftAndRightLungs.m)

  2. MANUAL STEP: inspect the outer boudaries of the left and right lungs and correct if necessary

  • Visualise the lung segmentation by selecting Lungs on the GUI. Each lung is assigned a label (colour)

    • Blue (RIGHT LUNG)
    • Green (LEFT LUNG)

  • You can make corrections on the outer lung boundaries, or the boudaries between lungs (if they are touching)

    • Select the Correct tab to edit the lung boudaries
      • Use the Edit Boundary tool to click on a new outer boudary point, shifting the whole boundary in 3D towards that point
      • Use the Paint tool to paint a whole 3D sphere in a lung colour
    • Once you manually edit a lung boundary, your manual segmentation will override all automated results for the lung segmentation. If you want to return to automated results you will need to delete all your corrections by clicking Delete edits

  1. Compute vesselness density (plugin code: PTKVesselDensity.m)

  2. Compute approximate lobe segmentaiton (plugin code: PTKLobesByVesselnessDensityUsingWatershed)

  • this uses the labelled airways to seed a watershed transform based on the vesselness density
  • The results of this are usually reasonably close to the true fissure. If they are very poor, it is often due to an incorrect airway labelling (see above step to manually correct airway labelling)
  • You can see the result of this approximation by enabling Developer mode and selecting Lobes/Lobes Initial Guess under the Plugins tab

  1. Compute fissureness based on Hessian transform (plugin code: PTKFissureness.m)

  2. Iteratively compute improved fissures (plugin code: PTKFissurenPlane.m)

  • These are computed by fitting points of high fissureness which lie in a region close to the previously computed approximate lobar boundaries, and smoothing the result using a multilevel B-spline

  1. Segment lobes using the new fissure plans - SEGMENT REGION/Lobes button on the gui (plugin code: PTKLobes.m)

  2. MANUAL STEP: inspect the boundaries between lobes and correct if necessary

  • Visualise the lobe segmentation by selecting Lobes on the GUI. Each lobe is assigned a label (colour)

    • Blue (RIGHT UPPER LOBE)
    • Green (RIGHT MIDDLE LOBE)
    • Cyan (RIGHT LOWER LOBE)
    • Magenta (LEFT UPPER LOBE)
    • Yellow (LEFT LOWER LOBE)

  • If the boundaries are highly inaccurate, you should check the airway labelling above and correct that before continuing to this step.

  • You can make small corrections on the boundaries between lobes

    • Select the Correct tab to edit the lobar boudaries
      • Use the Edit Boundary tool to click on a new boudary point, shifting the whole boundary in 3D towards that point
      • Use the Paint tool to paint a whole 3D sphere in a lobar colour
    • Once you manually edit a lobar boundary, your manual segmentation will override all automated results. If you want to return to automated results you will need to delete all your corrections by clicking Delete edits
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