Trabecular bone segmentation and calculation issue

Hi!! I am a new user of the BoneJ plugin. I am trying to segment the trabecular bone from the cortical bone of sheep mandibular sample, scanned with U-CT microCT. I used. nii files to work with BoneJ plugin in Fiji. I converted the original image files to 8-bit, adjusted the contrast and brightness followed by auto thresholding through out the slices. Then, I drew polygon ROI in each slice and used the interpolate ROIs option. Finally, clicking the plugin’s area/fraction option to get the BV, TV and BV/TV. However, it appears eventually that those numbers are not changing even if I change the ROIs and do the calculations in only few slices. I am sure that something is wrong with what I am doing but can’t understand how to solve it.

BoneJ does not respect ROIs for calculating Area/Volume fraction. It is likely that the numbers you are getting for BV and TV are the total number of foreground pixels in the image stack * pixel volume (BV) and total image volume (TV).

Better ROI handling is a long-term objective for the project.

Thanks Michael. I really appreciate it.

Could you please advise me on how I can segment the cortical bone from the trabecular bone? I need to calculate the bone morphometry for both cortical and trabecular bone, separately. I have been trying to follow the guidelines you have given in the BoneJ2 paper. But it’s not segmenting them. Sorry for the inconvenience.

Also, I want to calculate the Tr.Th, Tr.Sp etc. I used the thickness plug in but it’s not giving me any values or numbers