Postprocessing only bone image

[bsheshwor]

When I ran the inference file with bone images, I think it predicted all the other organs along with it. Can't I ignore other organs and only run inference and postprocessing code for bones only??

[alexanderjaus]

Hi @bsheshwor,
I’m not entirely sure what you mean by “bone imaging”—our networks were trained solely on CT, not bone scintigraphy.

Currently, there’s no option to predict only a subset of labels, as we use the default nnU-Net setup. The easiest workaround is to filter the predictions afterward. Alternatively, you could train a custom model using only the bone labels from the atlas dataset.

As for post-processing: since selective label prediction isn’t supported, the script also doesn’t handle single-label filtering by default. But you can easily modify it to ignore non-bone labels.