# New extension: Fully automatic whole-body CT segmentation in 2 minutes using TotalSegmentator

**URL:** <https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710>\
**Category:** Support\
**Tags:** feature, segmentation, ai\
**Created:** [December 13, 2022, 1:32pm UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710 "2022-12-13T13:32:08Z")\
**Posts on this page:** 20\
**Page:** 3

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**Author:** ![Xavier\_Tre](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/xavier_tre/32/18221_2.png) [@Xavier\_Tre](https://discourse.slicer.org/u/Xavier_Tre)\
**Post date:** [January 30, 2023, 4:24am UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/52 "2023-01-30T04:24:46Z")

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Hello, I have problems to install totalsegmentator, already I have read the document several times where, and I have made several attempts to install it without results. Can someone explain to me how to install it? a tutorial video?

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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:** [January 30, 2023, 7:55am UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/53 "2023-01-30T07:55:07Z")

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Please describe what you did, what you expected to happen, and what happened instead. Include screenshots and copy here all messages displayed in the log window of the TotalSegmentator module.

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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, 2:53pm UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/54 "2023-02-06T14:53:42Z")

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5 posts were split to a new topic: [Segment the body surface using sTotalSegmentator](https://discourse.slicer.org/t/segment-the-body-surface-using-stotalsegmentator/27666)

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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 15, 2023, 3:30am UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/55 "2023-02-15T03:30:51Z")

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A post was split to a new topic: [Export TotalSegmentator results to DICOM](https://discourse.slicer.org/t/export-totalsegmentator-results-to-dicom/27815)

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**Author:** ![zhang\_ming](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/zhang_ming/32/15790_2.png) [@zhang\_ming](https://discourse.slicer.org/u/zhang_ming)\
**Post date:** [February 20, 2023, 12:18pm UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/56 "2023-02-20T12:18:47Z")

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Will this plugin use our local weights to compute(refined or trained by my local dataset), and the weights uploaded to googledrive for users to download

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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:** [April 5, 2023, 7:58pm UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/57 "2023-04-05T19:58:22Z")

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2 posts were split to a new topic: [TotalSegmentator indicates that GTX 1060 GPU has not enough memory](https://discourse.slicer.org/t/totalsegmentator-indicates-that-gtx-1060-gpu-has-not-enough-memory/28766)

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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:** [April 5, 2023, 7:56pm UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/60 "2023-04-05T19:56:11Z")

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2 posts were split to a new topic: [Can TotalSegmentator capture deformities such as Can TotalSegmentator heterotopic ossification?](https://discourse.slicer.org/t/can-totalsegmentator-capture-deformities-such-as-can-totalsegmentator-heterotopic-ossification/28765)

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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:** [August 9, 2023, 5:42pm UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/62 "2023-08-09T17:42:25Z")

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A post was split to a new topic: [Run TotalSegmentator on MultiVolume](https://discourse.slicer.org/t/run-totalsegmentator-on-multivolume/31073)

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**Author:** ![Julius\_W](https://avatars.discourse-cdn.com/v4/letter/j/ea5d25/32.png) [@Julius\_W](https://discourse.slicer.org/u/Julius_W)\
**Post date:** [October 12, 2023, 1:00pm UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/63 "2023-10-12T13:00:46Z")

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Congratulation for implementing TotalSegmentator to Slicer. I use Slicer to segment bones of the lower extremities and wondered, if you are planning on implementing the v2.0 of TotalSegmentator as well? I would greatly appreciate this work as the segmentation of the lower extremity is enabled in this version.

Thank you very much  
Julius

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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:** [October 12, 2023, 3:44pm UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/64 "2023-10-12T15:44:40Z")

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Yes, it is planned to implement TotalSegmentator v2 as soon as possible.

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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:** [October 13, 2023, 4:54pm UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/65 "2023-10-13T16:54:41Z")

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We have a functional prototype in this [pull request](https://github.com/lassoan/SlicerTotalSegmentator/pull/38) of TotalSegmentator v2 in Slicer. We need to tune a few small things before we release it, probably in a week or so. If you don’t want to wait for that then you can get the updated TotalSegmentator.py and .ui files from github and overwrite the files in your Slicer installation folder.

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**Author:** ![Julius\_W](https://avatars.discourse-cdn.com/v4/letter/j/ea5d25/32.png) [@Julius\_W](https://discourse.slicer.org/u/Julius_W)\
**Post date:** [October 17, 2023, 11:17am UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/66 "2023-10-17T11:17:21Z")

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That’s great thank you!

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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:** [January 12, 2024, 4:44am UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/67 "2024-01-12T04:44:46Z")

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A post was split to a new topic: [Segmenting fractured bones](https://discourse.slicer.org/t/segmenting-fractured-bones/33746)

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**Author:** ![Luca1](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/luca1/32/69018_2.png) [@Luca1](https://discourse.slicer.org/u/Luca1)\
**Post date:** [January 18, 2024, 4:29pm UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/68 "2024-01-18T16:29:48Z")

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Is there any chance to use “total segmentator” with cone beam CT acquired with angiography systems in the body (liver)? Thanks

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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:** [January 18, 2024, 4:44pm UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/69 "2024-01-18T16:44:43Z")

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Yes, it works on CBCT images as well. However, if the image quality is very bad (which is not uncommon, especially for low-dose acquisitions) then the accuracy will suffer.

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**Author:** ![Tobias](https://avatars.discourse-cdn.com/v4/letter/t/c67d28/32.png) [@Tobias](https://discourse.slicer.org/u/Tobias)\
**Post date:** [February 11, 2024, 8:23pm UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/70 "2024-02-11T20:23:08Z")

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Hi,  
I am trying to make it run and when I look in pytorch utils it said torch version 1.8.1  
However, when i run the totalsegmentator it says that it needs to install a higher version of torch (1.12.1) and restart. And then it restarts but nothing happens.  
Does anyone have any idea what I am doing wrong?

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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 12, 2024, 3:03am UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/71 "2024-02-12T03:03:16Z")

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You have some old pytorch 1.x version in your pip cache that gets installed by default.

You can go to Pytorch Utils module, uninstall this old version, restart Slicer, go to Pytorch Utils module again, and before you click to install Pytorch, write `>=2` in the version requirement textbox.

These uninstall and install steps should be performed automatically if you use the latest Slicer Stable Release or latest Slicer Preview Release.

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**Author:** ![Sandra\_Garcia](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sandra_garcia/32/77036_2.png) [@Sandra\_Garcia](https://discourse.slicer.org/u/Sandra_Garcia)\
**Post date:** [June 19, 2024, 8:58am UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/72 "2024-06-19T08:58:11Z")

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Hi @lassoan I have a quick question.

I am interested in conducting an experimental campaign on the functionality of TotalSegmentator. For this purpose, I want to modify some parameters and compare the results obtained. I have tried to make modifications from within the program, but regarding segmentation, it is practically impossible to change anything. Therefore, I wanted to ask if there are parameters in the program’s code that can be modified to obtain different results from the same data set. For example, changing the resolution, edge detection, or something like that. If you have any ideas on how I can achieve this, I would greatly appreciate it. It doesn’t have to be something complex, just to be able to compare various results. Thank you in advance for your response.

Using CT images.

Thank you in advance for your response

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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:** [June 19, 2024, 11:47am UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/74 "2024-06-19T11:47:25Z")

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The result is anyways resampled in the end to the input image resolution, so if you want to change that then you can resample the input image before running TotalSegmentator.

This will not change things fundamentally, as the internal segmentation model had fixed resolution. You would need to retrain the entire model on higher-resolution data to get finer details.

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**Author:** ![carl](https://avatars.discourse-cdn.com/v4/letter/c/ee7513/32.png) [@carl](https://discourse.slicer.org/u/carl)\
**Post date:** [January 7, 2025, 7:59am UTC](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710/75 "2025-01-07T07:59:18Z")

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Hi,  
has anyone tried this with situs inversus or situs ambiguus patients?  
i will give that a try on a mac studio. No idea if the M4 is supported.

[Previous page](https://discourse.slicer.org/t/new-extension-fully-automatic-whole-body-ct-segmentation-in-2-minutes-using-totalsegmentator/26710.md?page=2)

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