Segment the body surface using TotalSegmentator

Hi, I love this helpful extension!
I found that subset - body skin(torso) segmentation is now available!
I am wondering if I can use that subset function on 3D Slicer program too. Is there anyone tried segmenting skin on 3D Slicer with total segmentator?
Is it possible to use skin segmentation function after upgrade version of total segmentator?

Hi, body/skin and pleural/pericardial effusion will probably be integrated into the TotalSegmentator extension very soon. @lassoan, just give me a short note if you want me to do this.

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Thank you for the reply! I am looking forward to use new additional functions!

Just see that body/skin and effusions special tasks are already implemented in the TotalSegmentator extension. Please just update the extension via the extension manager.

“Body trunc” segmentation with an A10G GPU and 24 GB video RAM:

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@lassoan I can not yet get skin segmentation working - is there a special trick?

Which “Segmentation task” does not do what you expect?

Subtasks refers to a body: body, body_trunc, body_extremities, skin task but I only get “body_trunc” and “body_extremities” segmentations when I run our extensions “body” task, not “skin”:

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Effusions work great.

These are the segmentation tasks made avilable in the Slicer extension:

If you find that something does not work in the Slicer extension that it is a good place to discuss here. If there is something wrong/unexpected in the TotalSegmentator Python package then probably the best is to create an issue directly in Issues · wasserth/TotalSegmentator · GitHub (and post the link to the issue here for reference).

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I’ve had a look and it seems that only 2 of the 4 segments produced by the task is listed in the class map of the task. I’ve submitted an issue to TotalSegmentator Python package to clarify:

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I´ve just tested the latest TotalSegmentator release from the command line and it produces “body.nii.gz” and “skin.nii.gz” into the segmentation folder, but it appears this has already been realized :slight_smile:

image

Yes, we just don’t read the two extra files because they are not listed in the task outputs.

Jakob replied in the github issue telling that the two extra segments are derived by some simple additional image processing operations. So, I think we’ll just keep returning the two original segments in the Slicer extension (and not the derived ones).

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How can this skin labelmap be downloaded/ added as one of the segments?

To get a “skin” (body surface) segment, you can go to TotalSegmentator module, choose Segmentation taskbody, and click Apply.