How can I solve the threshold problem?

I want to calculate the cranial bone volume of the defect model.

The picture with the red boundary and yellow arrow is the bone I want to calculate.

After I applied the threshold (Method: Default; Background: Black), the image converted to the picture with the blue boundary.

It seemed it calculates the all-white region of the stack. (The value is 62%)

How can I solve the threshold problem?

Hi
@Jeffrey
To help you :
Are you allowed to deposit one or even two images?
An original and another where is found the organ that you want to study.

Draw a rectangular ROI containing the bone and soft tissue around it but not the air, then try the autothreshold again. The air pixels are making the histogram shift to the left because there are a lot of them (and very few bone pixels), so the autothreshold algorithm is segmenting between air and not air. You want to give pixels to the autothrehold with only the two phases where you need a boundary - for you that’s between soft tissue and bone.

you can also manually set a threshold if you have a good estimate of the bone pixel values: if your imaging is consistent that may be more reliable than an autothreshold, which is sensitive to the relative amounts of the tissue types in the image due to the way they fall in the histogram.