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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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Outputs of lung vessel segmentation #71

Closed Chen-Jxiang closed 1 year ago

Chen-Jxiang commented 1 year ago

Hi,

I noticed that when I run the lung vessel segmentation, I got a mask that contains small real values (~10^-7 - 10^-2). What do these values mean? If I want to get a binary mask, how should I choose the threshold?

Thanks, Junxiang

wasserth commented 1 year ago

That is strange. You can threshold the mask at 0.5 to get a binary mask.

Chen-Jxiang commented 1 year ago

OK. If I use other thresholds like 5^-5, the mask looks reasonable. However, if I use 0.5, none of the points in the image is above the thresholds.

wasserth commented 1 year ago

What is the command you are using to call TotalSegmentator?

Chen-Jxiang commented 1 year ago

This is how I call TotalSegmentor: TotalSegmentator -i [filename] --fast -o [output] TotalSegmentator -i [filename] -ta lung_vessels -o [output]

wasserth commented 1 year ago

This works fine for me and the output mask (lung_vessels.nii.gz) is a binary mask with 0 and 1.