Separating Cortical and Trabecular Bone

Separation of the cortical and trabecular bone is the most critical step for the accurate quantification of selected morphometric indices. Two methods — Kohler and Buie — are available for separating cortical and trabecular bone. The input of the automated segmentation is a bone segmentation in which bone mineralization is present and a filled region of interest in which the bone segmentation are filled (see Segmenting and Filling Bone). The output of the process is two regions of interest listed below:

Cortical bone… The intersection of the cortical area with the input bone segmentation.

Trabecular bone… The intersection of the trabecular area with the input bone segmentation.

Segmentation methods and settings
  Description
Segmentation method Two methods — Kohler and Buie — are available for segmenting cortical and trabecular bone.

Kohler… This segmentation method relies on basic image processing concepts using morphological and other operators to separate cortical from trabecular bone. Refer to Kohler et el, Automated compartmental analysis for high-throughput skeletal phenotyping in femora of genetic mouse models, Bone, 41, 4, (659-667), (2007) for details about this method.

Note In general, the Kohler method works best on single, regularly-shaped bone specimens. In addition, the initial bone segmentation must be closed on all sides (see Capping an Initial Bone Segmentation).

Buie… This dual threshold method to segment bone regions usually produces accurate and repeatable results. Refer to Buie et al, Automatic segmentation of cortical and trabecular compartments based on a dual threshold technique for in vivo micro-CT bone analysis, Bone, 41, 4, (505-515), (2007) for details about this method.
Trabecular thickness The expected maximal thickness of the trabeculae (trabecularThickness) in your sample should be entered here.

Recommendations You can measure trabecular thickness with the Ruler tool (see Using the Ruler Tool) or you can generate a thickness mesh from a sub-sample of the trabeculae and then find the maximum thickness of the mesh (see Exporting ROIs and Multi-ROIs to Thickness Meshes).
How to Separate Cortical and Trabecular Bone
  1. Advance to the Filled Bone Separation page of the Bone Analysis Wizard.
  2. Select the region of interests that will provide the inputs for segmenting cortical and trabecular bone in the Bone and Filled bone drop-down menus.

    You can select the filled region of interest that you created in the previous step, an edited region of interest, or any other region of interest that satisfies the required criteria.

  3. Choose a segmentation method — Kohler or Buie — to segment cortical and trabecular bone.
  4. Enter the expected maximal thickness of the trabeculae in the Trabecular thickness edit box.
  5. Click the Segment button to start the automated segmentation routine.

    Do the following if you selected the Kohler method:

    • Use the slider to select a threshold to separate cortical and trabecular bone, as shown below.

    • Click OK to apply the selected threshold.
  6. Wait for the automated segmentation to be completed.

    At the end of the process, two new regions of interest — Cortical bone and Trabecular bone — appear in the Data Properties and Settings panel.

  7. Verify the accuracy of the cortical and trabecular bone segmentations, recommended.

  8. Edit the regions of interest, if required (see Editing Cortical and Trabecular Segmentations).
  9. Click Next to continue to the Global Measurements page (see Computing Global Measurements).

In some cases, an automated segmentation may result in voxels corresponding to trabecular bone erroneously labeled as cortical bone, as circled below, or vice versa.

Automated segmentation result

If required, you can automatically re-assign labeled voxels from one region to interest to another with the Brush tools by working in Exclusive mode. In this mode, only the labeled voxels belonging to the selected regions of interest will be affected when painting. You can also use any of the other ROI Painter tools, such as the Smart Grid tool, to edit an automated segmentation (see ROI Painter).

How to Re-Assign Labeled Voxels with the Brush Tools
  1. Select the 2D view on which you plan to edit the regions of interest.
  2. Select the two regions of interest in the Data Properties and Settings panel.

    The two regions of interest are identified as (A) and (B). For example, '(A) Trabecular bone of BoneROI' and '(B) Cortical bone of BoneROI'. When painting, you can re-assign voxels labeled as trabecular bone to those labeled as cortical bone and vice-versa.

  3. Select Single slice or Multi-slice in the 2D view tools panel.
  4. Select a Brush type — Round or Square.
  5. Check the Exclusive option, circled below.

    Note In this mode, painting will only be applied to the labeled voxels of the selected regions of interest. Unlabeled voxels will not be painted.

  6. Do the following, as required:
    • Re-assign labeled voxels to ROI (A) from ROI (B) by holding down Left Ctrl (or your configured Add with key) and then painting.

    • Re-assign labeled voxels from ROI (A) to ROI (B) by holding down Left Shift (or you configured Remove with key) and then painting.