Hello, I have been working with CT scans from several skeletal populations and have recently run into a problem with the Moments of Inertia stage in the BoneJ plugin.
For some of the populations I have been working with, the following protocol has worked to attain cross sectional area measurements:
First a DICOM stack of the CT scans is imported into ImageJ and the scale of the image is recorded. The stack is then exported as a TIFF stack and opened in Avizo. As these scans contain multiple elements very close together, Avizo is used to crop each 3D model to just a singular bone of interest. This is done using the volume edit module and a padding value is added if necessary. The cropped element is then exported as a 2D TIFF stack and reopened in ImageJ. In ImageJ, the original scale from the DICOM file is entered and the image is made 8-bit. Then, using the BoneJ plugin, Moments of Inertia is run to properly orient the bone. The threshold is then adjusted, and slice geometry of the bone’s midslice is run to attain the cross sectional area.
For three out of approximately ten populations I have processed with this procedure it has worked without issue. However, for the remaining populations, the cropping of the image seems to be creating a problem. When I export the cropped image from Avizo and then open the image in ImageJ, the Moments of Inertia calculation produces a bone surrounded by a semi-opaque cloud, thus making CSA measurement impossible. I have tried multiple things to get rid of the ‘cloud,’ including adjusting the Brightness/Contrast settings of the original DICOM file in ImageJ before exporting it as a TIFF and cropping it in Avizo. This does get rid of the cloud around the bone, but when I run MOI on the cropped TIFF in ImageJ, the volume and mass outputs are about triple what would be expected. The same thing happens when I try the Subtract Background command in ImageJ.
Does anyone know how this could be fixed? I am told that the cloud surrounding the bone could be an issue stemming from the CT scanner’s original settings, thus making differentiation between the bone and the background poor. However, attempting to adjust the padding value has not fixed the issue. Is there a way to get rid of the cloud without interfering with the accuracy of the slice geometry output values?