Need help for Femur segmentation

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Ali Vali

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Sep 25, 2026, 10:19:02 AMSep 25

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Hi everyone,

I'm segmenting a femur from a hip CT in ITK-SNAP 4.4.0. The semi-automatic (snake) tool keeps leaking from the femur into the pelvis at the hip joint. The two bones touch there and have similar, high density — I measured about 325–354 at the contact point, which is higher than any threshold I've tried (100, 150, 200). So thresholding alone can't separate them.

I painted a manual barrier along the joint gap using a separate "Barrier" label, and set Paint over to Clear Label before running the evolution step. It still crosses through.

My ROI has 106 slices and the joint is a curved 3D surface, so I'm not sure if I just didn't paint the barrier on enough slices, or if I'm missing something else. Is there a recommended way to separate two touching bones of similar density, or a faster way to build a barrier across many slices than painting each one by hand?

Thanks for any pointers.

Ali

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