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wasserth / TotalSegmentator

Tool for robust segmentation of >100 important anatomical structures in CT and MR images
Apache License 2.0
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CT skull segmentation fills hole in the skull #362

Closed pajdakovicm closed 2 weeks ago

pajdakovicm commented 3 weeks ago

Holes are present in my CT scans. However, when I perform a skull segmentation, the holes get filled. Any way to resolve this issue?

wasserth commented 2 weeks ago

Can you post some images? Otherwise I do not really understand what you mean.

pajdakovicm commented 2 weeks ago

The holes are present in images due to the operation that treats subdural hematoma, see attached image. I suppose the holes get filled because the training data did not contain such images?

Screenshot 2024-09-09 at 11 37 15
wasserth commented 2 weeks ago

Thanks for the image. Your assumption is correct. You could do thresholding within the TotalSegmentator skull mask to get a segmentation where the hole is not filled.

pajdakovicm commented 2 weeks ago

Thank you for your answer. What exactly do you mean by "thresholding within the TotalSegmentator skull mask to get a segmentation" ?