# Segment the body surface using TotalSegmentator

**URL:** <https://discourse.slicer.org/t/segment-the-body-surface-using-totalsegmentator/27666>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [February 6, 2023, 10:20am UTC](https://discourse.slicer.org/t/segment-the-body-surface-using-totalsegmentator/27666 "2023-02-06T10:20:57Z")\
**Posts on this page:** 14\
**Page:** 1

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**Author:** ![SoYoung\_Lim](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/soyoung_lim/32/18295_2.png) [@SoYoung\_Lim](https://discourse.slicer.org/u/SoYoung_Lim)\
**Post date:** [February 6, 2023, 10:20am UTC](https://discourse.slicer.org/t/segment-the-body-surface-using-totalsegmentator/27666/1 "2023-02-06T10:20:57Z")

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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?

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [February 6, 2023, 10:47am UTC](https://discourse.slicer.org/t/segment-the-body-surface-using-totalsegmentator/27666/2 "2023-02-06T10:47:47Z")

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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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**Author:** ![SoYoung\_Lim](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/soyoung_lim/32/18295_2.png) [@SoYoung\_Lim](https://discourse.slicer.org/u/SoYoung_Lim)\
**Post date:** [February 6, 2023, 10:51am UTC](https://discourse.slicer.org/t/segment-the-body-surface-using-totalsegmentator/27666/3 "2023-02-06T10:51:16Z")

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

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [February 6, 2023, 1:19pm UTC](https://discourse.slicer.org/t/segment-the-body-surface-using-totalsegmentator/27666/4 "2023-02-06T13:19:26Z")

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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:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/8/688d2a1060fc642b2730cc64e7f929522b520743.jpeg)

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [February 6, 2023, 2:51pm UTC](https://discourse.slicer.org/t/segment-the-body-surface-using-totalsegmentator/27666/5 "2023-02-06T14:51:19Z")

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

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [February 6, 2023, 2:55pm UTC](https://discourse.slicer.org/t/segment-the-body-surface-using-totalsegmentator/27666/6 "2023-02-06T14:55:50Z")

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

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**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [February 6, 2023, 3:48pm UTC](https://discourse.slicer.org/t/segment-the-body-surface-using-totalsegmentator/27666/7 "2023-02-06T15:48:03Z")

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[Subtasks](https://github.com/wasserth/TotalSegmentator#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”:

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/2/625de1b3acc171be5abf5342d038104148e022c8.png)

Effusions work great.

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [February 6, 2023, 4:04pm UTC](https://discourse.slicer.org/t/segment-the-body-surface-using-totalsegmentator/27666/8 "2023-02-06T16:04:50Z")

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

> <https://github.com/lassoan/SlicerTotalSegmentator/blob/d9b4f6e7a2eae05d099836aa8d314a59df066262/TotalSegmentator/TotalSegmentator.py#L308-L314>

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](https://github.com/wasserth/TotalSegmentator/issues) (and post the link to the issue here for reference).

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [February 6, 2023, 4:21pm UTC](https://discourse.slicer.org/t/segment-the-body-surface-using-totalsegmentator/27666/9 "2023-02-06T16:21:54Z")

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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:

> <https://github.com/wasserth/TotalSegmentator/issues/67>
>
> When using the \`body\` task then the network computes 4 segments:
> \- skin.nii.gz
> …
> \- body.nii.gz
> \- body\_trunc.nii.gz
> \- body\_extremities.nii.gz
> 
> However, in the class map only "body\_trunc" and "body\_extremities" show up:
> 
> https://github.com/wasserth/TotalSegmentator/blob/af44342d7b5a7f6331b33b26434b58882871a68a/totalsegmentator/map\_to\_binary.py#L311-L313
> 
> Is this just a bug or we should get the list of segments a task produces in some other way?

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<div class="post-metadata">

**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [February 6, 2023, 5:43pm UTC](https://discourse.slicer.org/t/segment-the-body-surface-using-totalsegmentator/27666/10 "2023-02-06T17:43:29Z")

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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 🙂

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/8/0/807baed1f99048046348f936c4f405f157d9dd5a.png)

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [February 6, 2023, 6:50pm UTC](https://discourse.slicer.org/t/segment-the-body-surface-using-totalsegmentator/27666/11 "2023-02-06T18:50:30Z")

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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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**Author:** ![Aayush\_Agrawal\_ch21b](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/aayush_agrawal_ch21b/32/69900_2.png) [@Aayush\_Agrawal\_ch21b](https://discourse.slicer.org/u/Aayush_Agrawal_ch21b)\
**Post date:** [April 4, 2024, 8:39am UTC](https://discourse.slicer.org/t/segment-the-body-surface-using-totalsegmentator/27666/12 "2024-04-04T08:39:15Z")

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

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [April 4, 2024, 3:44pm UTC](https://discourse.slicer.org/t/segment-the-body-surface-using-totalsegmentator/27666/13 "2024-04-04T15:44:58Z")

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

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<div class="post-metadata">

**Author:** ![liam26](https://avatars.discourse-cdn.com/v4/letter/l/858c86/32.png) [@liam26](https://discourse.slicer.org/u/liam26)\
**Post date:** [January 15, 2026, 5:24am UTC](https://discourse.slicer.org/t/segment-the-body-surface-using-totalsegmentator/27666/14 "2026-01-15T05:24:25Z")

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I’m having the same issue. Were you able to resolve this?