Cortical/trabecular percentage using Volume Fraction (BoneJ)



Hi everyone, I’m new in the Forum and I am writing in order to receive some advices on the procedure to calcolate the bone fraction in an image stack of 685 slices. My aim is to obtain the percentage of cortical bone volume over the entire bone volume. I’ve been following this procedure so far: import the image sequence, applying the right threshold and then tick the BoneJ option Volume Fraction. (In the volume fraction dialog box I choose the voxel algorithm and tick Use ROI MANAGER ) . Although I am not sure about the results. I explain myself better: it looks to me that the total volume considered is not of the total volume of the bone but of the bounding box that surrounds it. This way the percentage of the cortical bone is altered. Could anyone give me some suggestions ? Thanks in advanced Kind Regards


Could you please indicate that this is a BoneJ-question?





Don’t worry - I added a tag to this post for “BoneJ” … hopefully those developers (@mdoube & @rimadoma) of this plugin will see this post - for sure they can better assist you.

It would be best if you could also include more information… what is it that you are not sure of regarding the results? Also - if you can attach the original images you are working with - would be best to get you the help you need.

eta :slight_smile:


Thank you! I will add more information on the original post.



You have the right idea: the plugin (either voxel or surface) compares the ratio of total bone volume to total image stack volume. What you could try is to use a different threshold to mask out non-cortical bone, and then compare those results to running volume fraction on all the bone.

Best regards,


Thank you so much for your replying. I will follow the suggestion. Meantime what I did was to invert the colour image, considering this way bone as black and background as white. This way it looks to me it could give a better ratio bone volume/total volume. Kind Regards