Segmenting and Filling Bone

An initial bone segmentation is required to guide the automated cortical and trabecular segmentation process for generating the inputs for computing morphometric indices and mappings of anisotropy and volume fraction. In most cases, the initial bone segmentation region of interest can be extracted from a threshold range (see Creating Threshold Segmentations) applied to the image data, as described below.

1. Pre-process your image data, as required (see Data Preprocessing).
2. Right-click the image data from the required bone study in the Data Properties and Settings panel and then choose Bone Analysis Wizard in the pop-up to open the Bone Analysis Wizard.

   The image data appears in a 2 by 2 layout in the Bone Analysis Wizard.

3. Adjust window leveling, as required (see Window Leveling).
4. Select the BoneROI region of interest on the Data Properties and Settings panel, as shown below.

   

5. Click the Segment tab on the left sidebar to access the ROI Tools panel.
6. Do the following to create a region of interest with data values thresholded for bone:
   • Select the Define range option in the Range box on the ROI Tools panel, as shown below.

     

   • Make sure that the required image data is selected in the Image drop-down menu.

   • Drag the left and/or right Range sliders to change the minimum and/or maximum values of the intensity range or enter the required values in the Selected range Min and Max edit boxes.

     

     Note You can also make your adjustments on a histogram of the image data, as shown below.

     

     Note You can also create an unbiased segmentation by clicking the Lower Otsu or Upper Otsu button.

   • Verify the selected range on other images in the image stack and in other views of the data, recommended.

     

   • Click the Add button to label all voxels that fall within the selected range.

     

     Information about the region of interest is displayed on the Data Properties and Settings panel (see ROI Properties and Settings).

7. Uncheck the Define range option in the Range box.
8. Continue to the next section to learn how to refine the region of interest, if required.

In some cases, an initial threshold bone segmentation may contain unwanted objects, such as mounting aids, stray pixels, and noise. These issues should be addressed before you continue a bone analysis workflow.

You can apply the Process Islands options to remove unwanted objects, as described below, or you can use the ROI Painter tools to manually edit a threshold bone segmentation (see ROI Painter).

1. Right-click the region of interest in the Data Properties and Settings panel and then choose Refine Region of Interest > Process Islands in the pop-up menu.

   

2. Choose the required sub-menu item (see Processing Islands).

   For example, you can isolate the largest object or objects in the region of interest by choosing Isolate (6-connected) nth First Biggest and then selecting the number of objects you want to keep.

The first step in processing an initial segmentation of mineralized bone is to create a filled region of interest that fully describes the cortical and trabecular areas. To properly fill a bone segmentation, you must make sure that it is first capped on all sides. For example, a bone shaft that may be open at one end after cropping.

1. Scroll to the image slice that shows the most proximal or distal view of the open shaft, as shown below.

   

   Note In some cases, you may have to create an oblique view to cap the segmentation (see Creating Oblique Views).

2. Click the Segment tab on the left sidebar to access the ROI Painter panel.
3. Select Single slice on the 2D views panel.

   

4. Do the following to cap the initial segmentation with the Brush tools:
   • Select the Round Brush or Square Brush tool, as required.
   • Select Full as the Brush type in the drop-down menu.
   • Hold down Left Crtl, or your configured Add with key, on your keyboard. The cursor is now a painting brush.
   • Change the diameter of the brush by rotating your mouse scroll wheel, as required.
   • While holding down Left Crtl and your left mouse button, paint the area inside the region of interest.

     

     Note You can remove areas from a region of interest by holding down Left Shift while painting.

     Note You can also any of the other tools on the ROI Painter panel to cap the initial segmentation (see ROI Painter).

Closing the holes in an initial bone segmentation, including cortical pores and vascular canal inlets, and filling the inner areas of the segmentation, is required for separating cortical and trabecular bone.

Cortical pore (circled)

The output of this process is a filled region of interest, which is an input for separating cortical and trabecular bone.

Region of interest (Filled)… The segmentation of the filled area corresponding to the bone cortex and the marrow in which the holes of the bone segmentation are closed.

1. Make sure that the region of interest is capped on all sides (see Capping an Initial Bone Segmentation).
2. Enter the required threshold distance to close the cortical pores and vascular canal inlets in the Close holes smaller than edit box.

   

3. Click the Fill button to start the automated routine.
4. Wait for the process to be completed.

   At the end of the process, a new region of interest 'BoneROI (Filled)' appears in the Data Properties and Settings panel.

   

5. Verify the accuracy of the result, recommended.

   

6. Edit the filled region of interest, if required.

   See ROI Painter and other topics in Segmentation Tools for information about the segmentation tools available in Dragonfly for editing ROIs.

7. Click Next to continue to the next segmentation step (see Separating Cortical and Trabecular Bone).