# \#totalsegmentator

**URL:** https://discourse.slicer.org/tag/totalsegmentator/480.md

[Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md)

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## [Soft-tissue segmentation: advice needed](https://discourse.slicer.org/t/soft-tissue-segmentation-advice-needed/48060)

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**Author:** [@Toumia\_Bessedik](https://discourse.slicer.org/u/Toumia_Bessedik)\
**Replies:** 0\
**Last updated:** [September 3, 2026, 10:20pm UTC](https://discourse.slicer.org/t/soft-tissue-segmentation-advice-needed/48060 "2026-09-03T22:20:55Z")

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Hello, I would like to get your opinion on an approach I am currently using to refine the segmentation of soft tissues in a head MRI. I used TotalSegmentator (MR) to automatically segment the soft tissues, particularly…

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## [Segment tooth enamel and pulp from TotalSegmentator tooth-by-tooth](https://discourse.slicer.org/t/segment-tooth-enamel-and-pulp-from-totalsegmentator-tooth-by-tooth/47637)

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**Author:** [@r\_vorup](https://discourse.slicer.org/u/r_vorup)\
**Replies:** 4\
**Last updated:** [July 19, 2026, 6:11pm UTC](https://discourse.slicer.org/t/segment-tooth-enamel-and-pulp-from-totalsegmentator-tooth-by-tooth/47637 "2026-07-19T18:11:58Z")

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Hello all, I have used the TotalSegmentator to segment a CBCT scan of upper and lower jaw, and have gotten each tooth in an individual segment. I now want to split each tooth into dentine and enamel, for them to be 3D p…

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## [download fails/freezes on both direct connection and VPN (with academic license activated)](https://discourse.slicer.org/t/download-fails-freezes-on-both-direct-connection-and-vpn-with-academic-license-activated/47346)

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**Author:** [@Tomy\_Roster](https://discourse.slicer.org/u/Tomy_Roster)\
**Replies:** 2\
**Last updated:** [July 13, 2026, 5:17pm UTC](https://discourse.slicer.org/t/download-fails-freezes-on-both-direct-connection-and-vpn-with-academic-license-activated/47346 "2026-07-13T17:17:59Z")

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I am using the TotalSegmentator extension in 3D Slicer to extract muscle and fat compartments using the tissue\_4\_types subtask. I have already successfully obtained and activated my academic license key. However, I am c…

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## [Total Segmentator Extension Fails Installation on Slicer 5.12.0](https://discourse.slicer.org/t/total-segmentator-extension-fails-installation-on-slicer-5-12-0/47468)

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**Author:** [@amyers](https://discourse.slicer.org/u/amyers)\
**Replies:** 2\
**Last updated:** [July 7, 2026, 3:08pm UTC](https://discourse.slicer.org/t/total-segmentator-extension-fails-installation-on-slicer-5-12-0/47468 "2026-07-07T15:08:02Z")

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On Windows 11, I just installed Slicer 5.12.0 revision 34621, built 2026-06-24. I was able to install DentalSegmentator, SlicerOpenAnatomy, NNUnet, etc; however, TotalSegmentator failed to install. This is the error I r…

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## [TotalSegmentator Partial Segmentation](https://discourse.slicer.org/t/totalsegmentator-partial-segmentation/47335)

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**Author:** [@Arash1](https://discourse.slicer.org/u/Arash1)\
**Replies:** 3\
**Last updated:** [June 15, 2026, 2:46pm UTC](https://discourse.slicer.org/t/totalsegmentator-partial-segmentation/47335 "2026-06-15T14:46:54Z")

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Any suggestions on why the segment is like this? \[DEBUG\]\[Qt\] 14.06.2026 13:36:34 (unknown:0) - Session start time …: 20260614\_133634 \[DEBUG\]\[Qt\] 14.06.2026 13:36:34 (unknown:0) - Slicer version …: 5.10.0 (revision…

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## [HighRes segmentation in TotalSegmentator](https://discourse.slicer.org/t/highres-segmentation-in-totalsegmentator/47345)

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**Author:** [@jordy86](https://discourse.slicer.org/u/jordy86)\
**Replies:** 0\
**Last updated:** [June 15, 2026, 12:40pm UTC](https://discourse.slicer.org/t/highres-segmentation-in-totalsegmentator/47345 "2026-06-15T12:40:22Z")

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I noticed some test high res models in the TotalSegmentator github a while back but now they are gone. Are there any plans to introduce higher resolution segmentation similar to the highresh heart chambers available now? …

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## [Ported mlx version of TotalSegmentator - Apple Silicon](https://discourse.slicer.org/t/ported-mlx-version-of-totalsegmentator-apple-silicon/47213)

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**Author:** [@pox\_got](https://discourse.slicer.org/u/pox_got)\
**Replies:** 0\
**Last updated:** [June 2, 2026, 2:58pm UTC](https://discourse.slicer.org/t/ported-mlx-version-of-totalsegmentator-apple-silicon/47213 "2026-06-02T14:58:22Z")

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Please check it out and provide feedback.

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## [Help Non-linear Transform Error During Crop Volume / Total Segmentation](https://discourse.slicer.org/t/help-non-linear-transform-error-during-crop-volume-total-segmentation/46989)

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**Author:** [@jimenagonzalezsal](https://discourse.slicer.org/u/jimenagonzalezsal)\
**Replies:** 1\
**Last updated:** [May 11, 2026, 10:03pm UTC](https://discourse.slicer.org/t/help-non-linear-transform-error-during-crop-volume-total-segmentation/46989 "2026-05-11T22:03:02Z")

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Hi everyone!! I wanted to ask for some help. I’m trying to crop a volume and then add Total Segmentation, but whenever I try to either crop or create the segmentation from an MRI, a message appears stating: “Output volu…

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## [TotalSegmentator fails to install PyTorch dependencies – installTorch() got unexpected keyword argument 'torchVisionVersionRequirement'](https://discourse.slicer.org/t/totalsegmentator-fails-to-install-pytorch-dependencies-installtorch-got-unexpected-keyword-argument-torchvisionversionrequirement/46911)

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**Author:** [@Madison\_Golledge](https://discourse.slicer.org/u/Madison_Golledge)\
**Replies:** 9\
**Last updated:** [May 5, 2026, 11:40am UTC](https://discourse.slicer.org/t/totalsegmentator-fails-to-install-pytorch-dependencies-installtorch-got-unexpected-keyword-argument-torchvisionversionrequirement/46911 "2026-05-05T11:40:08Z")

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I’m trying to use the TotalSegmentator extension in 3D Slicer for segmenting an MRI dataset, but I’m running into a consistent error during the dependency installation step. When clicking “Apply” in the TotalSegmentator…

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## [TotalSegmentator Error on CT](https://discourse.slicer.org/t/totalsegmentator-error-on-ct/46757)

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**Author:** [@ranahashemi](https://discourse.slicer.org/u/ranahashemi)\
**Replies:** 1\
**Last updated:** [April 16, 2026, 4:44pm UTC](https://discourse.slicer.org/t/totalsegmentator-error-on-ct/46757 "2026-04-16T16:44:46Z")

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Hi everyone, I am using TotalSegmentator for a bone segmentation on CT scan DICOM files which I extracted from Ga68-PSMA PET/CT of our patients, the problem is the extension is working with some patients and then with th…

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## [Problem with TotalSegmentator - my computer freezes](https://discourse.slicer.org/t/problem-with-totalsegmentator-my-computer-freezes/46068)

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**Author:** [@jimenagonzalezsal](https://discourse.slicer.org/u/jimenagonzalezsal)\
**Replies:** 2\
**Last updated:** [February 15, 2026, 2:08pm UTC](https://discourse.slicer.org/t/problem-with-totalsegmentator-my-computer-freezes/46068 "2026-02-15T14:08:29Z")

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Hello! I need help. I’m trying to segment lumbar spine DICOMs, but whenever I click Apply, my computer freezes and the segmentation never finishes.

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## [Total Segmentator error: Failed to compute results...returned non-zero exit status 1](https://discourse.slicer.org/t/total-segmentator-error-failed-to-compute-results-returned-non-zero-exit-status-1/36322)

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**Author:** [@liyiranran2001](https://discourse.slicer.org/u/liyiranran2001)\
**Replies:** 4\
**Last updated:** [January 23, 2026, 3:12am UTC](https://discourse.slicer.org/t/total-segmentator-error-failed-to-compute-results-returned-non-zero-exit-status-1/36322 "2026-01-23T03:12:43Z")

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Operating system:windows11 Slicer version:5.6.2 Hi, I have installed Pytorch and other python packages properly, and restarted and reinstalled Slicer for several times. No matter I choose the ‘fast’ mode or not, the p…

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## [TotalSegmentator finishes successfully but Slicer GUI freezes on macOS (M2-Pro Sequoia) after completion](https://discourse.slicer.org/t/totalsegmentator-finishes-successfully-but-slicer-gui-freezes-on-macos-m2-pro-sequoia-after-completion/45753)

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**Author:** [@Lennart99](https://discourse.slicer.org/u/Lennart99)\
**Replies:** 2\
**Last updated:** [January 12, 2026, 6:46pm UTC](https://discourse.slicer.org/t/totalsegmentator-finishes-successfully-but-slicer-gui-freezes-on-macos-m2-pro-sequoia-after-completion/45753 "2026-01-12T18:46:24Z")

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Hi everyone, I am using the TotalSegmentator extension in slicer to segment MRI data. The data is successfully loaded and apparently segmented, however, before loading the segments into slicer and making them accessible…

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## [Segmentation does not fit into new geometry](https://discourse.slicer.org/t/segmentation-does-not-fit-into-new-geometry/35691)

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**Author:** [@SHMMU](https://discourse.slicer.org/u/SHMMU)\
**Replies:** 5\
**Last updated:** [December 4, 2025, 10:31pm UTC](https://discourse.slicer.org/t/segmentation-does-not-fit-into-new-geometry/35691 "2025-12-04T22:31:08Z")

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I have used total segmentator to aquire liver volume. However, when I go to export the file as NIFTI I get this error message, “the current segmentation does not completely fit into the new geometry. Do you want to cr…

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## [TotalSegmentator: Failed to install required packages ](https://discourse.slicer.org/t/totalsegmentator-failed-to-install-required-packages/38405)

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**Author:** [@gsmattay](https://discourse.slicer.org/u/gsmattay)\
**Replies:** 13\
**Last updated:** [October 27, 2025, 8:22pm UTC](https://discourse.slicer.org/t/totalsegmentator-failed-to-install-required-packages/38405 "2025-10-27T20:22:17Z")

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Operating system: MacOS Big Sur 11.4 Slicer version: 5.6.2 Hello, I have installed Slicer, installed Pytorch version 2.2.2 via the Pytorch utils module, installed the 3d segmentator module, and restarted Slicer. When …

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## [TotalSegmentator License Activation Issues](https://discourse.slicer.org/t/totalsegmentator-license-activation-issues/34866)

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**Author:** [@KewilB](https://discourse.slicer.org/u/KewilB)\
**Replies:** 13\
**Last updated:** [October 11, 2025, 8:23am UTC](https://discourse.slicer.org/t/totalsegmentator-license-activation-issues/34866 "2025-10-11T08:23:44Z")

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I recently obtained a license in order to use the heartchambers highres option. I am unable to activate my license. When I put the code sent to my email in the python console, I get a syntax error. Not sure if this is th…

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## [When I finish processing in TotalSegmentator, "Show 3d" is not clickable](https://discourse.slicer.org/t/when-i-finish-processing-in-totalsegmentator-show-3d-is-not-clickable/44721)

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**Author:** [@cp15](https://discourse.slicer.org/u/cp15)\
**Replies:** 1\
**Last updated:** [October 10, 2025, 12:35pm UTC](https://discourse.slicer.org/t/when-i-finish-processing-in-totalsegmentator-show-3d-is-not-clickable/44721 "2025-10-10T12:35:04Z")

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When I finsih processing a file, it says processing complete and there are no errors listed. I am unable to toggle the “show 3d” button. I’m nor sure what I’m missing.

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## [TotalSegmentator Licensed Tasks Not Appearing in 3D Slicer Interface](https://discourse.slicer.org/t/totalsegmentator-licensed-tasks-not-appearing-in-3d-slicer-interface/43523)

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**Author:** [@Guilherme\_Augusto](https://discourse.slicer.org/u/Guilherme_Augusto)\
**Replies:** 2\
**Last updated:** [September 22, 2025, 1:59am UTC](https://discourse.slicer.org/t/totalsegmentator-licensed-tasks-not-appearing-in-3d-slicer-interface/43523 "2025-09-22T01:59:54Z")

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TotalSegmentator Licensed Tasks Not Appearing in 3D Slicer Interface Problem Description I have TotalSegmentator v2.10.0 installed and working via Python API in 3D Slicer 5.7.0, but licensed tasks like thigh\_shoulder\_…

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## [How to edit segmentations in total segmentator](https://discourse.slicer.org/t/how-to-edit-segmentations-in-total-segmentator/35498)

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**Author:** [@jake14](https://discourse.slicer.org/u/jake14)\
**Replies:** 7\
**Last updated:** [September 20, 2025, 10:27pm UTC](https://discourse.slicer.org/t/how-to-edit-segmentations-in-total-segmentator/35498 "2025-09-20T22:27:09Z")

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Used total segmentor for one case and there was an incorrect segmentation done where it has a gap in a structure I am intersted in. Is there an easy was to correct and edit the segmentation that is not accurate? every ot…

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## [TotalSegmentator No Output](https://discourse.slicer.org/t/totalsegmentator-no-output/44433)

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**Author:** [@aceegreene](https://discourse.slicer.org/u/aceegreene)\
**Replies:** 7\
**Last updated:** [September 13, 2025, 7:29pm UTC](https://discourse.slicer.org/t/totalsegmentator-no-output/44433 "2025-09-13T19:29:25Z")

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Hi everyone - I am trying to use totalsegmentator to segment an MRI image I have and seem to not be getting any results. There seem to be no errors in the module itself or in the Python console but once the processing i…

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## [TotalSegmentator error: \`returned non-zero exit status 1\`](https://discourse.slicer.org/t/totalsegmentator-error-returned-non-zero-exit-status-1/43932)

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**Author:** [@era\_888](https://discourse.slicer.org/u/era_888)\
**Replies:** 3\
**Last updated:** [August 9, 2025, 7:40pm UTC](https://discourse.slicer.org/t/totalsegmentator-error-returned-non-zero-exit-status-1/43932 "2025-08-09T19:40:29Z")

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Failed to compute results. Command ‘\[‘E:/Slicer 5.8.1/bin/../bin\\PythonSlicer.EXE’, ‘E:\\Slicer 5.8.1\\lib\\Python\\Scripts\\TotalSegmentator.exe’, ‘-i’, ‘C:/Users/msi/AppData/Local/Temp/Slicer/\_\_SlicerTemp\_\_2025-08-01\_17+24…

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## [TotalSegmentator failed to compute – ModuleNotFoundError: No module named 'skimage.morphology'](https://discourse.slicer.org/t/totalsegmentator-failed-to-compute-modulenotfounderror-no-module-named-skimage-morphology/43577)

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**Author:** [@Mael](https://discourse.slicer.org/u/Mael)\
**Replies:** 0\
**Last updated:** [July 2, 2025, 2:40pm UTC](https://discourse.slicer.org/t/totalsegmentator-failed-to-compute-modulenotfounderror-no-module-named-skimage-morphology/43577 "2025-07-02T14:40:14Z")

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Hi everyone, I’m trying to use the TotalSegmentator extension in 3D Slicer, but I get an error when I try to compute the segmentation. The error message is: ModuleNotFoundError: No module named 'skimage.morphology' I…

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## [nnUNET failed to load segmentation in DentalSegmentator & totalSegmentator](https://discourse.slicer.org/t/nnunet-failed-to-load-segmentation-in-dentalsegmentator-totalsegmentator/43374)

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**Author:** [@chz31](https://discourse.slicer.org/u/chz31)\
**Replies:** 6\
**Last updated:** [June 17, 2025, 6:41pm UTC](https://discourse.slicer.org/t/nnunet-failed-to-load-segmentation-in-dentalsegmentator-totalsegmentator/43374 "2025-06-17T18:41:00Z")

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I am using Ubuntu 22.04 and Slicer 5.9.0. The DentalSegmentator showed “failed to load segmentation; something is wrong with nnUnet processing” Here is the error log: \[DEBUG\]\[Qt\] 16.06.2025 15:08:12 \[\] (unknown:0) -…

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## [Segmenting a stomach after gastric sleeve](https://discourse.slicer.org/t/segmenting-a-stomach-after-gastric-sleeve/43391)

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**Author:** [@SanneGr](https://discourse.slicer.org/u/SanneGr)\
**Replies:** 0\
**Last updated:** [June 17, 2025, 4:36pm UTC](https://discourse.slicer.org/t/segmenting-a-stomach-after-gastric-sleeve/43391 "2025-06-17T16:36:46Z")

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Hi! I really like the TotalSegmentator extension in 3D Slicer. As of now, I’m trying to segment the stomach after gastric sleeve surgery. This surgery results in a smaller stomach with a different shape and this leads t…

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## [Can't install Total Segmentor](https://discourse.slicer.org/t/cant-install-total-segmentor/43313)

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**Author:** [@kopachini](https://discourse.slicer.org/u/kopachini)\
**Replies:** 3\
**Last updated:** [June 13, 2025, 6:40am UTC](https://discourse.slicer.org/t/cant-install-total-segmentor/43313 "2025-06-13T06:40:17Z")

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Hello everyone. It seems I can’t install Total segmentor. I used it on my older, less powerful laptop but fast version, but now I am not able to install it. This is the error I get. I have Lenovo Legion i9 14900HX …

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## [Failure to Compute Results using TotalSegmentator (returned non-zero exist status 1)](https://discourse.slicer.org/t/failure-to-compute-results-using-totalsegmentator-returned-non-zero-exist-status-1/42927)

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**Author:** [@tjlotz](https://discourse.slicer.org/u/tjlotz)\
**Replies:** 2\
**Last updated:** [May 15, 2025, 4:22pm UTC](https://discourse.slicer.org/t/failure-to-compute-results-using-totalsegmentator-returned-non-zero-exist-status-1/42927 "2025-05-15T16:22:47Z")

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Hello Slicer Support! I have been trying to run TotalSegmentator, but it has been failing. The Slicer Error message that I have been receiving states, “… returned non-zero exit status 1.” Can you please help me underst…

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## [TotalSegmentator returned non-zero exit status 1](https://discourse.slicer.org/t/totalsegmentator-returned-non-zero-exit-status-1/42876)

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**Author:** [@imer\_T](https://discourse.slicer.org/u/imer_T)\
**Replies:** 0\
**Last updated:** [May 11, 2025, 1:44pm UTC](https://discourse.slicer.org/t/totalsegmentator-returned-non-zero-exit-status-1/42876 "2025-05-11T13:44:57Z")

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\[CRITICAL\]\[Stream\] 11.05.2025 15:02:37 (unknown:0) - subprocess.CalledProcessError: Command ‘\[‘E:/04-INSTALL\_2/Slicer 5.8.1/bin/../bin\\PythonSlicer.EXE’, ‘E:\\04-INSTALL\_2\\Slicer 5.8.1\\lib\\Python\\Scripts\\TotalSegmentator…

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## [What modalities and protocols TotalSegmentator works with?](https://discourse.slicer.org/t/what-modalities-and-protocols-totalsegmentator-works-with/42779)

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**Author:** [@angeek](https://discourse.slicer.org/u/angeek)\
**Replies:** 1\
**Last updated:** [May 3, 2025, 2:42pm UTC](https://discourse.slicer.org/t/what-modalities-and-protocols-totalsegmentator-works-with/42779 "2025-05-03T14:42:05Z")

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Hello, is there any specific recommendations concerning the modality. Does TotalSegmentator work well on CT Scans with/without injection, and for MRI, which kind is prefered (T1,T2,STIR,Flair,inPhase) ? Thanks

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## [TotalSegmentator + Slicer 5.8.1 - "ModuleNotFoundError: No module named 'pydicom.pixels'"](https://discourse.slicer.org/t/totalsegmentator-slicer-5-8-1-modulenotfounderror-no-module-named-pydicom-pixels/42386)

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**Author:** [@jochoaTX](https://discourse.slicer.org/u/jochoaTX)\
**Replies:** 2\
**Last updated:** [April 1, 2025, 12:05am UTC](https://discourse.slicer.org/t/totalsegmentator-slicer-5-8-1-modulenotfounderror-no-module-named-pydicom-pixels/42386 "2025-04-01T00:05:06Z")

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Operating system: WinPro 11 Slicer version: 5.8.1 Expected behavior: TotalSegmentator to totally segment Actual behavior: Pukes I’ve declared defeat. Cannot solve this myself. It seems that TotalSegmentator may be lo…

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## [TotalSegmentator choose organs to be segmented](https://discourse.slicer.org/t/totalsegmentator-choose-organs-to-be-segmented/42270)

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**Author:** [@MihaiPomohaci](https://discourse.slicer.org/u/MihaiPomohaci)\
**Replies:** 0\
**Last updated:** [March 23, 2025, 8:43pm UTC](https://discourse.slicer.org/t/totalsegmentator-choose-organs-to-be-segmented/42270 "2025-03-23T20:43:41Z")

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Operating system: Windows 11 Slicer version: 5.8.1 Hello, First of all I would like to thank you guys for this app that makes my life so much easier, and also a huge thanks to the TotalSegmentator team! I am doing a …

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