Erosion Volume Module
The Erosion Volume module segments the bone erosions on a greyscale scan based on user-plotted seed points and the periosteal bone mask. It then calculates the volume, surface area, and shape parameters of those erosions. The periosteal bone mask can be created in the AutomaticContour Module if it is not already available.
Load the greyscale scan, and the contour/mask if available, into Slicer. Either drag-and-drop the files to the application window, or hit the Add Data button
and select the files. The contour/mask need to be loaded as LabelMapVolumes. Check the Show Options check box at the top right corner of the Add Data prompt window, and check the LabelMap option.
In this step, erosions are identified by placing seed points in each of them. It is recommended to plot seed points in all the erosions first, and then run this step one or more times, each time with different parameters, depending on the quality of the output.
Parameters:
- Input Volume: the greyscale scan.
- Input Contour: the periosteal bone mask.
- Output Erosions
- Lower/Upper Threshold: global thresholds, in Scanco intensity units.
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Seed Points: To place a seed point, hit the placement button
, and left click in the viewer windows where that seed point should go. Manage the seed points using the seed point table, and right click the selected seed point to access more actions. Place seed points in the middle of the erosions (one or more seed points per erosion). Try to keep all the seed points as middle in the erosions as possible.
- Large Erosions: Check this box if the seed points are plotted in "large" erosions that are not bounded by regular bone. This determines the internal parameters used in the segmentation. There is not a standard for what is considered "large erosions". It is recommended to run Step 4 several times and adjust the parameters based on the output.
- Advanced Parameters: Further adjust those internal segmentation parameters. The Minimum Erosion Radius specifies the erosion separation, which is the radius of the sphere that can be contained by the narrowest part of the erosion. The Dilate/Erode Distance is the dilate/erode distance used in the internal morphological operations in order to remove connection between erosion and trabecular space.
Once all the parameters are set, hit the Get Erosions button.
If the output does not capture some erosion well, rerun this step with different Advanced parameters. Do not overwrite the old Output Erosions. Instead, create a new output at Output Erosions to store the new erosion segmentations.
If the output contains trabecular leakage, increase the values of the Advanced parameters. If some erosions are missing despite being indicated by some seed points, decrease the values of the Advanced parameters, adjust the seed point locations, or add new seed points.
Erosions from Step 4 can be manually corrected and combined into a single output.
Parameters:
- Segmentation: the output from Step 4.
- Master Volume: the greyscale scan.
For each output from Step 4, Remove undesired erosion segmentations by selecting the erosion segmentation (e.g. "Erosion_1") and hitting the Remove button. The segmentation in the top row named "MASK_Keep_Invisible" is the periosteal bone mask. Manually correct the remaining erosion segmentations. The editor is set so that only low-intensity voxels inside the periosteal bone mask are editable.
The good erosion segmentations may scatter among multiple outputs. They can be combined into a single output using Copy Segmentation. In one of the windows, create a new output to hold all the finalized erosion segmentations. In the other window, select the segmentations to be copied, and hit the arrow button.
Optionally, convert the finialized output to a LabelMapVolume using Export Segmentation. Segmentation in Slicer can only be saved as an NRRD or Nifti file, while LabelMapVolume can be saved in more file formats.
Parameters:
- Input Erosions: Should contain all the finialized erosions
- Master Volume: The greyscale scan.
- Voxel Size: the CT voxel size in millimetres, 0.0820 for XTremeCT I and 0.0607mm for XtremeCT II.
- Output Table: Only erosions in the selected Input Erosions will appear in the Output Table.
Once all the parameters are set, hit the Get Statistics button. Supported statistics include volume, surface area, roundness, and coordinates of each erosion. Hover the mouse over an erosion in the viewer window to see its name. The erosion names should match the corresponding seed point numbers.
Hit the Save button
in the tool bar, and select the files to be saved. It is recommended to save the MRML Scene with the file extension .mrml. To reload the files into Slicer, load the MRML Scene, and the other files will be automatically loaded into Slicer.
