# \#monai-auto3dseg

**URL:** https://discourse.slicer.org/tag/monai-auto3dseg/496.md

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## [Automatic segmentation of the ventricles (brain)](https://discourse.slicer.org/t/automatic-segmentation-of-the-ventricles-brain/45915)

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**Author:** [@Preetham\_Dange](https://discourse.slicer.org/u/Preetham_Dange)\
**Replies:** 7\
**Last updated:** [March 5, 2026, 8:11am UTC](https://discourse.slicer.org/t/automatic-segmentation-of-the-ventricles-brain/45915 "2026-03-05T08:11:07Z")

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Hello everyone, I am currently working on hydrocephalus . I wanted to automatically segment the ventricles (brain) and use the volume statistics for research purposes. I tried MONAI Auto3Dseg and nnUnet but I couldn’t f…

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## [MONAI Auto3DSeg – inconsistent performance for vertebral body segmentation](https://discourse.slicer.org/t/monai-auto3dseg-inconsistent-performance-for-vertebral-body-segmentation/46081)

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**Author:** [@jchao](https://discourse.slicer.org/u/jchao)\
**Replies:** 1\
**Last updated:** [February 8, 2026, 4:31pm UTC](https://discourse.slicer.org/t/monai-auto3dseg-inconsistent-performance-for-vertebral-body-segmentation/46081 "2026-02-08T16:31:36Z")

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Hi everyone, I’m currently working with Prof. Ron Alkalay on a spine CT segmentation project using MONAI Auto3DSeg and would appreciate any advice from the community. My task is to segment only vertebral bodies. I refo…

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## [Error when running MONAI Auto3DSeg (cannot import name ‘MetaKeys’ from ‘monai.utils’)](https://discourse.slicer.org/t/error-when-running-monai-auto3dseg-cannot-import-name-metakeys-from-monai-utils/35738)

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**Author:** [@davidngqk88](https://discourse.slicer.org/u/davidngqk88)\
**Replies:** 5\
**Last updated:** [July 9, 2025, 4:37pm UTC](https://discourse.slicer.org/t/error-when-running-monai-auto3dseg-cannot-import-name-metakeys-from-monai-utils/35738 "2025-07-09T16:37:22Z")

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Am testing it on some abdominal CT datasets now. am getting errors saying ImportError: cannot import name ‘MetaKeys’ from ‘monai.utils’ ‘Processing failed with return code 1’ after it attempts to create the segmentat…

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## [How to convert series (IM files) to one file](https://discourse.slicer.org/t/how-to-convert-series-im-files-to-one-file/41269)

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**Author:** [@amirzadeh](https://discourse.slicer.org/u/amirzadeh)\
**Replies:** 1\
**Last updated:** [May 28, 2025, 3:02am UTC](https://discourse.slicer.org/t/how-to-convert-series-im-files-to-one-file/41269 "2025-05-28T03:02:14Z")

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Hi. My MRI and CT-Angio images are in a PATH that includes many series folders with IM files that don’t have any extensions. When I add the PATH to 3d slicer it load the images in different series like the images that I’…

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## [AI Segmentation error with MOOSE (non zero exit status, check the FOV) and MONAIAuto3DSeg](https://discourse.slicer.org/t/ai-segmentation-error-with-moose-non-zero-exit-status-check-the-fov-and-monaiauto3dseg/42761)

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**Author:** [@j\_bu](https://discourse.slicer.org/u/j_bu)\
**Replies:** 3\
**Last updated:** [May 1, 2025, 6:29pm UTC](https://discourse.slicer.org/t/ai-segmentation-error-with-moose-non-zero-exit-status-check-the-fov-and-monaiauto3dseg/42761 "2025-05-01T18:29:50Z")

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Hello all, I want to compare different segemantations but I always get exceptions. Please help, thank you very much in advance. Total Segmentator works. After opening my CT scan I get the output: “\[VTK\] There is more t…

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## [MONAI Auto3DSeg inference sources](https://discourse.slicer.org/t/monai-auto3dseg-inference-sources/36929)

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**Author:** [@wesselk](https://discourse.slicer.org/u/wesselk)\
**Replies:** 1\
**Last updated:** [June 21, 2024, 7:32pm UTC](https://discourse.slicer.org/t/monai-auto3dseg-inference-sources/36929 "2024-06-21T19:32:37Z")

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Hi all, I have been working with the new MONAI Auto3DSeg and have a few questions if someone could help me out: 1- Where can I find the source for the models used? For example, “Madiastinal anatomy TS2” is not in MONA…

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## [Strategies for Batch/Sequential segmentation of 3D volumes with MONAI Auto3DSeg?](https://discourse.slicer.org/t/strategies-for-batch-sequential-segmentation-of-3d-volumes-with-monai-auto3dseg/40844)

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**Author:** [@Yue-Hin\_Loke1](https://discourse.slicer.org/u/Yue-Hin_Loke1)\
**Replies:** 0\
**Last updated:** [December 25, 2024, 3:59am UTC](https://discourse.slicer.org/t/strategies-for-batch-sequential-segmentation-of-3d-volumes-with-monai-auto3dseg/40844 "2024-12-25T03:59:03Z")

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Hi there, I’ve been able to create a Python extension that loops automatically uses Auto3DSeg to automatically segments multiple .nrrd files sequentially. I do notice that the turnround time can be long (~ 1.5 minute …

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## [When running slicer.cli.run, an error occurs.](https://discourse.slicer.org/t/when-running-slicer-cli-run-an-error-occurs/40317)

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**Author:** [@fallen\_leaves](https://discourse.slicer.org/u/fallen_leaves)\
**Replies:** 0\
**Last updated:** [November 21, 2024, 10:17pm UTC](https://discourse.slicer.org/t/when-running-slicer-cli-run-an-error-occurs/40317 "2024-11-21T22:17:18Z")

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When running slicer.cli.run, an error occurs. As shown below: The code is shown in the figure Could you please tell me how to solve this?

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## [Facial muscle segmentation using MONAI Auto3DSeg](https://discourse.slicer.org/t/facial-muscle-segmentation-using-monai-auto3dseg/35734)

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**Author:** [@philippepellerin](https://discourse.slicer.org/u/philippepellerin)\
**Replies:** 27\
**Last updated:** [November 15, 2024, 9:54am UTC](https://discourse.slicer.org/t/facial-muscle-segmentation-using-monai-auto3dseg/35734 "2024-11-15T09:54:51Z")

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Greetings. Much congratulations! As a professional in the field of medical imaging and segmentation, your work on the thorax, abdomen, and brain is undoubtedly significant. However, I believe that your expertise could a…

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## [MONAI AutoSeg3D\_Hip & spine](https://discourse.slicer.org/t/monai-autoseg3d-hip-spine/39715)

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**Author:** [@Label\_Map\_AI](https://discourse.slicer.org/u/Label_Map_AI)\
**Replies:** 1\
**Last updated:** [October 22, 2024, 7:08am UTC](https://discourse.slicer.org/t/monai-autoseg3d-hip-spine/39715 "2024-10-22T07:08:36Z")

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Hello, I attempted automatic segmentation using MONAI’s Auto3Dseg, and while it generally works well, I’ve encountered an issue. When reviewing the results, the right pelvis region appears on the left side of the mask, …

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## [Error when using Brain Tumor Segmentation(GLI)" model in MONAI Auto3DSeg](https://discourse.slicer.org/t/error-when-using-brain-tumor-segmentation-gli-model-in-monai-auto3dseg/38484)

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**Author:** [@clam\_keep](https://discourse.slicer.org/u/clam_keep)\
**Replies:** 2\
**Last updated:** [September 23, 2024, 7:40am UTC](https://discourse.slicer.org/t/error-when-using-brain-tumor-segmentation-gli-model-in-monai-auto3dseg/38484 "2024-09-23T07:40:34Z")

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I was try to use the “Brain Tumor Segmentation(GLI)” model in the MONAI Auto3DSEG to create segmentations on my own MRdata. It do worked once and then keep failing. These are error messages: Processing started Writing…

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## [MONAI AutoSeg3D head and neck Model ](https://discourse.slicer.org/t/monai-autoseg3d-head-and-neck-model/37426)

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**Author:** [@Alisha](https://discourse.slicer.org/u/Alisha)\
**Replies:** 0\
**Last updated:** [July 17, 2024, 11:00am UTC](https://discourse.slicer.org/t/monai-autoseg3d-head-and-neck-model/37426 "2024-07-17T11:00:58Z")

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I want to get the segmentations(ex. cord, parotid gland, thyroid gland etc.) by using MONAI. Are there any head and neck models for MONAI AutoSeg3D?

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## [Is MONAI Auto3DSeg Whole body segmentation model based on SegResNet?](https://discourse.slicer.org/t/is-monai-auto3dseg-whole-body-segmentation-model-based-on-segresnet/37255)

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**Author:** [@samuelholly](https://discourse.slicer.org/u/samuelholly)\
**Replies:** 1\
**Last updated:** [June 17, 2024, 10:01am UTC](https://discourse.slicer.org/t/is-monai-auto3dseg-whole-body-segmentation-model-based-on-segresnet/37255 "2024-06-17T10:01:47Z")

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Dear all, just a quick question: is the Whole body segmentation TS1 (v1.0.0) model based on the SegResNet architecture? Is there a paper describing this model? Thank you in advance. Best regards Samuel

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## [MONAI and TotalSegmentator](https://discourse.slicer.org/t/monai-and-totalsegmentator/36636)

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**Author:** [@khajta](https://discourse.slicer.org/u/khajta)\
**Replies:** 9\
**Last updated:** [July 2, 2024, 2:25am UTC](https://discourse.slicer.org/t/monai-and-totalsegmentator/36636 "2024-07-02T02:25:54Z")

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What is the difference between using MONAI Auto3DSeg and TotalSegmentor for automatic segmentation? There is also TotalSegmentator in MONAI Auto3DSeg.

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## [MONAI auto3dseg for pigs](https://discourse.slicer.org/t/monai-auto3dseg-for-pigs/37040)

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**Author:** [@Matteboo](https://discourse.slicer.org/u/Matteboo)\
**Replies:** 3\
**Last updated:** [June 28, 2024, 9:40am UTC](https://discourse.slicer.org/t/monai-auto3dseg-for-pigs/37040 "2024-06-28T09:40:57Z")

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Hello, First of all, it’s been one year that I’ve been using 3DSlicer and I want to thanks everyone for this amazing tool and for their help in this forum :smile: We are looking for a way to automatically segment the o…

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## [Lung segmentation using monai auto3dseg on matlab](https://discourse.slicer.org/t/lung-segmentation-using-monai-auto3dseg-on-matlab/37054)

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**Author:** [@sasurgan](https://discourse.slicer.org/u/sasurgan)\
**Replies:** 2\
**Last updated:** [June 27, 2024, 3:11am UTC](https://discourse.slicer.org/t/lung-segmentation-using-monai-auto3dseg-on-matlab/37054 "2024-06-27T03:11:38Z")

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I want to use the monai auto3dseg lung model on matlab, I could not find the pre-trained model on the internet. I can access it as model.pt from the Slicer 3D cache folder but I am not sure how to use it. Can anyone help…

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## [Monai label - edit a pre-trained model](https://discourse.slicer.org/t/monai-label-edit-a-pre-trained-model/35943)

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**Author:** [@ILB](https://discourse.slicer.org/u/ILB)\
**Replies:** 1\
**Last updated:** [May 17, 2024, 10:38pm UTC](https://discourse.slicer.org/t/monai-label-edit-a-pre-trained-model/35943 "2024-05-17T22:38:51Z")

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Hi there! I’ve recently started working with Monai Label on 3D Slicer to train a new model from scratch. My question is: would it be possible to use an already trained model, such as the "“wholeBody\_ct\_segmentation” an…

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## [Batch processing with MONAI Auto3DSeg extension module](https://discourse.slicer.org/t/batch-processing-with-monai-auto3dseg-extension-module/35993)

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**Author:** [@Osson4](https://discourse.slicer.org/u/Osson4)\
**Replies:** 1\
**Last updated:** [May 8, 2024, 6:32pm UTC](https://discourse.slicer.org/t/batch-processing-with-monai-auto3dseg-extension-module/35993 "2024-05-08T18:32:09Z")

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I am working on a set of around 60 CTs and I would like to process the volumes with the same model (brain and hemorrage) from the new monai Auto3dSeg extension module. While I can process them one by one within the GUI,…

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## [How to make a portable slicer with Monai Auto3Dseg extension](https://discourse.slicer.org/t/how-to-make-a-portable-slicer-with-monai-auto3dseg-extension/35815)

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**Author:** [@Osson4](https://discourse.slicer.org/u/Osson4)\
**Replies:** 1\
**Last updated:** [April 29, 2024, 8:44pm UTC](https://discourse.slicer.org/t/how-to-make-a-portable-slicer-with-monai-auto3dseg-extension/35815 "2024-04-29T20:44:26Z")

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Using the latest preview of slicer (5.7.0 revision 32834 built 2024-04-28) on a Windows system, I would like to try the new extension on a offline, hospital computer with limited space and writing rights but with good GP…