# The shaft center

Hi there! So glad I’ve found this forum!

I have CT-scans of dog tibias and femurs, the aim of my current study is to calculate the cross-section area in the middles of all the bones. Firstly I conduct the moment of inertia analysis, the way of aligning bones along the axes. The free space around the bone doesn’t matter, right? The program uses densities to identify where the bone is, and where is a “dark matter”, am I right?) And I don’t have to choose the bone including slices precisely, right? After that, it shows me the 3d model with the blue perpendicular lines in the center. Is that a geometrical center of the bone, can it ne used as a middle of the shaft? It’s very important for me, because I want to make the results comparable. If so, why it doesn’t show the center sometimes? What it depends on? At the second step I go to slice geometry and find the measurements of the slice near the center, which was calculated at the previous step (this center is also shown at the cross-sections of the new-opened window). Here I have another question, what is the angle between the cut and the shaft? Is it perpendicular to every slice?

That’s correct, provided that the pixel values outside the bone are less than the minimum threshold value that you set.

That’s correct.[quote=“Mitya_Vasyukov, post:1, topic:4417”]
Is that a geometrical center of the bone
[/quote]
Yes, it’s the centroid.

Yes.

I don’t know. An image that illustrates your issue would be helpful.

Approximately, and close to perpendicular if the bone is not curved and regular in shape.

If you scanned the bone with its long axis parallel to the scan axis, so that it is already closely aligned to the image z-axis, you don’t have to do an alignment with the moments of inertia plugin.

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Thank you for the answer, Michael!

Approximately, and close to perpendicular if the bone is not curved and regular in shape.

If you scanned the bone with its long axis parallel to the scan axis, so that it is already closely aligned to the image z-axis, you don’t have to do an alignment with the moments of inertia plugin.

Well, I did scan the bones approximately parallel with the scan axis, but the bones are quite curved indeed, so as I can see, the cut is perpendicular to the long axis of the bone, but sometimes is not quite perpendicular from the lateral view. Is there any way to make it perpendicular in each slice? Otherwise, the cross-sectional area depends on the angle of cut, am I right?

Yes, but it’s quite hard to implement. You have to work out whether it’s worth it.

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