Hello,

well, to me it looks like you did a segmentation of "air" and then created the pore-network for it. The problem is that your "air" contains not only the internal pores, but also the air surrounding your object. You have to get rid of that, to be able to calculate the pore-network only for the internal air.

You can do all necessary steps inside Avizo.

I suggest that you create a mask of your object (i.e. a binary label-field containing the filled shape of your object), and then use that mask to mask-out the external air, e.g. using "Mask" or "Arithmetic".

For creating the mask, you could start with your segmentation, invert it (so that it contains the bone material), and then apply a morphological "Closing" (maybe followed by some "Erosion".

For segmenting only the internal air, you could also use the module "Ambient Occlusion". Here is the link to a short introductory video for it: https://www.youtube.com/watch?v=pup_alqYxOY&list=PLoxdPzacxPYjDVMD4tPCaVbuQjxYizr_g&index=64

I hope that helps ...

Kind regards,

Andreas

Andreas Staude Thank you so much for the suggestion. The way I did it was, I opened the tiff file and used the autothresholding operation. From the output, I used a separate operation to create the pore network. I am not sure how to create a mask and how to use that to distinguish the internal and external air.

I am going to try doing the steps and see what I can do. I am quite new to avizo. Can you please suggest some tutorial that might give me some insight how to do those? I appreciate your help so much. Thank you again

You might want to have a look into Avizo's User's Guide (accessible via "Help" in the main menu).

There is a section called "Advanced Image Processing, Segmentation and Analysis". The module "Closing" is e.g. mentioned in "Measuring a Catalyst".

But maybe the approach using "Ambient Occlusion" I mentioned above would be the easiest for your case.