How to create a hole in specific region of a 3D image

Hi, I have a 3D image of an eye orbit created from stack of 2D CT slides as this one :

As shown in the picture, there should be a small gap (highlighed in red) where nerves of eye passing through. However due to smoothing of the image, this gap is closed.

Now how can I recreate it again?

I am not sure if overlaying a 2D mask on related 2D slides will do. If yes, how can I create this mask using the highlighted region? I even don't know how to get this region out of the 3D image.

Grateful if anyone can help. Thanks!

[Matt J]

Why not just reduce the smoothing?

[Ringo Cheung]

Well, good question.

Actually the 3D image was created from a set of binary CT slides using imbinarize(). During imbinarize, the use of threshold value will make some pixel lost, as some of the bones inside the orbit are so thin. This creates some holes in the resulting 3D image.

So, some pre-processing was done using bwmorph() and the use of smooth3() can fill the holes too. Reducing smoothing will retain the holes which is undesirable.

Thanks.