# \#monailabel

**URL:** https://discourse.slicer.org/tag/monailabel/454.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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## [New extension: MONAI Auto3DSeg - raise the bar in AI medical image segmentation](https://discourse.slicer.org/t/new-extension-monai-auto3dseg-raise-the-bar-in-ai-medical-image-segmentation/35680)

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**Author:** [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)\
**Replies:** 21\
**Last updated:** [March 3, 2026, 5:02pm UTC](https://discourse.slicer.org/t/new-extension-monai-auto3dseg-raise-the-bar-in-ai-medical-image-segmentation/35680 "2026-03-03T17:02:52Z")

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New extension: MONAI Auto3DSeg - raise the bar in AI medical image segmentation MONAI Auto3DSeg extension is a collaboration between MONAI and 3D Slicer developer teams (led by Andres Diaz Pinto - NVIDIA and Andras Lasso…

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## [Slicer error in getting segmentation when using monai label](https://discourse.slicer.org/t/slicer-error-in-getting-segmentation-when-using-monai-label/35477)

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**Author:** [@Sheng-xc](https://discourse.slicer.org/u/Sheng-xc)\
**Replies:** 4\
**Last updated:** [October 24, 2025, 2:39am UTC](https://discourse.slicer.org/t/slicer-error-in-getting-segmentation-when-using-monai-label/35477 "2025-10-24T02:39:58Z")

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Hi, I am working with Slicer5.6.2 and MONAILabel on my mac, using port forwarding from a Ubuntu server. The connection, server log, and client interface seem pretty good, but a slicer error raises everytime I try to g…

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## [Monai Label - Start with Labeled Dataset](https://discourse.slicer.org/t/monai-label-start-with-labeled-dataset/31801)

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**Author:** [@nasibov\_98](https://discourse.slicer.org/u/nasibov_98)\
**Replies:** 2\
**Last updated:** [October 20, 2025, 8:10am UTC](https://discourse.slicer.org/t/monai-label-start-with-labeled-dataset/31801 "2025-10-20T08:10:24Z")

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Hi, I would like to use my own labeled dataset to kickstart monai label training. Background: Followed the youtube installation and scribbler tutorial, i was able to download and view “Task09\_Spleen” in 3D slicer usin…

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## [Issues with multiple labels and masks overlapping in Monailabel](https://discourse.slicer.org/t/issues-with-multiple-labels-and-masks-overlapping-in-monailabel/44448)

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**Author:** [@koumeasa](https://discourse.slicer.org/u/koumeasa)\
**Replies:** 1\
**Last updated:** [September 29, 2025, 9:29am UTC](https://discourse.slicer.org/t/issues-with-multiple-labels-and-masks-overlapping-in-monailabel/44448 "2025-09-29T09:29:51Z")

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Hey everyone, I’m labeling brain segments in MONAILabel. The masks / ROIs used as input for Monailabel are a subselection extracted by slicerio.extract\_segments() function from a 3DSlicer Segmentation node. I modified …

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## [Saving a trained MONAILabel model.](https://discourse.slicer.org/t/saving-a-trained-monailabel-model/44186)

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**Author:** [@okkar\_kyaw](https://discourse.slicer.org/u/okkar_kyaw)\
**Replies:** 0\
**Last updated:** [August 24, 2025, 1:21am UTC](https://discourse.slicer.org/t/saving-a-trained-monailabel-model/44186 "2025-08-24T01:21:40Z")

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After annotations and and training the model. How do I save my already trained .pt file for later use and sharing between researcher ? Is there a buttom to do this?

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## [Monailabel X-ray 2D Segmentation Apps](https://discourse.slicer.org/t/monailabel-x-ray-2d-segmentation-apps/44105)

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**Author:** [@4Vaqrant](https://discourse.slicer.org/u/4Vaqrant)\
**Replies:** 0\
**Last updated:** [August 16, 2025, 11:57am UTC](https://discourse.slicer.org/t/monailabel-x-ray-2d-segmentation-apps/44105 "2025-08-16T11:57:10Z")

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I’m currently working on an X-ray segmentation project, aiming to perform semantic segmentation. My dataset is in .nii format and contains 3 different labels. I’ve completed the labeling process and now have around 60 l…

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## [Monailabel numpy.bool version conflict](https://discourse.slicer.org/t/monailabel-numpy-bool-version-conflict/43442)

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**Author:** [@chz31](https://discourse.slicer.org/u/chz31)\
**Replies:** 0\
**Last updated:** [June 20, 2025, 10:02pm UTC](https://discourse.slicer.org/t/monailabel-numpy-bool-version-conflict/43442 "2025-06-20T22:02:08Z")

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Hi, I installed monailabel in a conda environment using pip install -U monailabel following instructions: https://github.com/Project-MONAI/MONAILabel. My pytorch version is 2.6.0 with cu124. Python version is 3.9. Howe…

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## [MONAI Auto3DSeg Segmentation Error](https://discourse.slicer.org/t/monai-auto3dseg-segmentation-error/42594)

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**Author:** [@ShoopD](https://discourse.slicer.org/u/ShoopD)\
**Replies:** 1\
**Last updated:** [April 17, 2025, 12:55pm UTC](https://discourse.slicer.org/t/monai-auto3dseg-segmentation-error/42594 "2025-04-17T12:55:46Z")

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Greetings. I did a whole-body segmentation with the MONAI Auto3DSeg (Whole body segmentation TS1) and exported it in the RTSTRUCT format. There were a few missing parts after the segmentation, especially in the brain pa…

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## [MonaiLabel internal server error when running the model](https://discourse.slicer.org/t/monailabel-internal-server-error-when-running-the-model/42578)

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**Author:** [@chz31](https://discourse.slicer.org/u/chz31)\
**Replies:** 2\
**Last updated:** [April 16, 2025, 3:56am UTC](https://discourse.slicer.org/t/monailabel-internal-server-error-when-running-the-model/42578 "2025-04-16T03:56:06Z")

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Hi, I successfully trained a model using MonaiLabel for a simple skull segmentation. However, when I tested running the model on a volume, it reported Status: 500; Response: Internal Server Error Traceback (most recent…

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## [Problem installing radiology app of MonaiLabel in conda environment](https://discourse.slicer.org/t/problem-installing-radiology-app-of-monailabel-in-conda-environment/42567)

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**Author:** [@chz31](https://discourse.slicer.org/u/chz31)\
**Replies:** 1\
**Last updated:** [April 15, 2025, 6:33am UTC](https://discourse.slicer.org/t/problem-installing-radiology-app-of-monailabel-in-conda-environment/42567 "2025-04-15T06:33:32Z")

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Hi, I tried to reinstall monailabel in a fresh conda environment in Windows 11. Previously, I successfully installed monai and radiology app in a conda envrionment and ran in Slicer with no issue, but it suddenly could …

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## [How to Install Monai Label Server ANYWHERE](https://discourse.slicer.org/t/how-to-install-monai-label-server-anywhere/42004)

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**Author:** [@sad\_shovel](https://discourse.slicer.org/u/sad_shovel)\
**Replies:** 3\
**Last updated:** [March 17, 2025, 10:30pm UTC](https://discourse.slicer.org/t/how-to-install-monai-label-server-anywhere/42004 "2025-03-17T22:30:10Z")

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I cannot successfully install or connect to the monai label server anywhere through any means. I have tried: Google Collab My Local Machine VM through Google Cloud I’m losing my mind. Why is this so difficult? There …

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## [Monailabel issue - Internal Server Error](https://discourse.slicer.org/t/monailabel-issue-internal-server-error/39699)

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**Author:** [@Daniel\_Lo](https://discourse.slicer.org/u/Daniel_Lo)\
**Replies:** 3\
**Last updated:** [February 17, 2025, 10:57am UTC](https://discourse.slicer.org/t/monailabel-issue-internal-server-error/39699 "2025-02-17T10:57:49Z")

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Facing a few issues while using monailabel training. 1) \[Python\] Failed to run inference in MONAI Label Server. \[Python\] Message: Status: 500; Response: Internal Server Error Traceback (most recent call last): File …

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## [MONAILABEL all organs segmentation](https://discourse.slicer.org/t/monailabel-all-organs-segmentation/41682)

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**Author:** [@Maria\_Bota](https://discourse.slicer.org/u/Maria_Bota)\
**Replies:** 0\
**Last updated:** [February 13, 2025, 4:08pm UTC](https://discourse.slicer.org/t/monailabel-all-organs-segmentation/41682 "2025-02-13T16:08:43Z")

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Hello, I am runing the Monailabel radiology app inference. I want to be able to run inference just for a specific organ(e.g aorta) without looking for all organs. Is it possible to select the organ before running infere…

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## [Cannot start\_server for MONAILABEL](https://discourse.slicer.org/t/cannot-start-server-for-monailabel/27406)

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**Author:** [@Bor\_Antolic](https://discourse.slicer.org/u/Bor_Antolic)\
**Replies:** 3\
**Last updated:** [January 27, 2025, 6:11pm UTC](https://discourse.slicer.org/t/cannot-start-server-for-monailabel/27406 "2025-01-27T18:11:27Z")

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Hi! I hope someone could help me with my problem. I successfully installed Monailabel on my home (Mac)computer, started the server, and it works inside 3D Slicer. I followed same steps to install it on my work Windows co…

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## [Can't access MONAI Label server from 3D Slicer](https://discourse.slicer.org/t/cant-access-monai-label-server-from-3d-slicer/31301)

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**Author:** [@shihje](https://discourse.slicer.org/u/shihje)\
**Replies:** 11\
**Last updated:** [January 27, 2025, 6:10pm UTC](https://discourse.slicer.org/t/cant-access-monai-label-server-from-3d-slicer/31301 "2025-01-27T18:10:35Z")

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I’m trying to use 3D Slicer as a visualization tool for MONAI Label. I started up the MONAI Label server using the monailabel CLI in an SSH terminal, and got an IP address of the Uvicorn session: I then input this IP…

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## [Issue while starting the MONAILabel server](https://discourse.slicer.org/t/issue-while-starting-the-monailabel-server/25839)

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**Author:** [@deboshree\_roy](https://discourse.slicer.org/u/deboshree_roy)\
**Replies:** 2\
**Last updated:** [January 27, 2025, 6:09pm UTC](https://discourse.slicer.org/t/issue-while-starting-the-monailabel-server/25839 "2025-01-27T18:09:30Z")

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Problem report for Slicer 5.0.3 win-amd64: \[please describe expected and actual behavior\] While initializing the server an error message - \[2022-10-22 12:03:10,941\] \[2356\] \[MainThread\] \[INFO\] (uvicorn.error:59) - Appli…

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## [Validation\_set\_Accuracy in MONAILabel](https://discourse.slicer.org/t/validation-set-accuracy-in-monailabel/31027)

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**Author:** [@Spiros\_Karkavitsas](https://discourse.slicer.org/u/Spiros_Karkavitsas)\
**Replies:** 10\
**Last updated:** [November 14, 2024, 5:15pm UTC](https://discourse.slicer.org/t/validation-set-accuracy-in-monailabel/31027 "2024-11-14T17:15:07Z")

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Hello I am currently using MONAILabel extension with Slicer and I would like to ask how I can define which data is assigned for the calculation of the validation Dice similarity metric. I know I can adjust the percentag…

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## [Getting started with MONAIlabel](https://discourse.slicer.org/t/getting-started-with-monailabel/38559)

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**Author:** [@gendex](https://discourse.slicer.org/u/gendex)\
**Replies:** 2\
**Last updated:** [October 4, 2024, 1:56pm UTC](https://discourse.slicer.org/t/getting-started-with-monailabel/38559 "2024-10-04T13:56:36Z")

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Dear Slicer Community, I have been working with Slicer for a while now and have recently started using the MONAI module in Slicer. However, I’m having some issues getting the output that I’m looking for. I’ve managed t…

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## [Edit labels of DICOM images](https://discourse.slicer.org/t/edit-labels-of-dicom-images/38213)

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**Author:** [@erlendAQK](https://discourse.slicer.org/u/erlendAQK)\
**Replies:** 1\
**Last updated:** [September 5, 2024, 8:04am UTC](https://discourse.slicer.org/t/edit-labels-of-dicom-images/38213 "2024-09-05T08:04:05Z")

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I haved used Monailabel to label my images. I need to edit the labeling but have problems loading the labels on top of the image. This is how it looks like when I press “Submit Label” When I load the label it looks l…

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## [Openslide-python not working when trying to use monailabel](https://discourse.slicer.org/t/openslide-python-not-working-when-trying-to-use-monailabel/33427)

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**Author:** [@Vineet\_Saravanan](https://discourse.slicer.org/u/Vineet_Saravanan)\
**Replies:** 6\
**Last updated:** [August 20, 2024, 3:42am UTC](https://discourse.slicer.org/t/openslide-python-not-working-when-trying-to-use-monailabel/33427 "2024-08-20T03:42:31Z")

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When I try to install monailabel with the command ‘pip install -U monailabel’, I get this issue: I pip installed openslide-python before, but I am still having an issue. I also tried installing it with a GitHub clone…

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## [Failed to fetch Sample from MONAI Label Server.](https://discourse.slicer.org/t/failed-to-fetch-sample-from-monai-label-server/37735)

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**Author:** [@sowwn](https://discourse.slicer.org/u/sowwn)\
**Replies:** 0\
**Last updated:** [August 6, 2024, 2:07pm UTC](https://discourse.slicer.org/t/failed-to-fetch-sample-from-monai-label-server/37735 "2024-08-06T14:07:43Z")

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Hello everyone, Can you guys help me with this issue? I deploy the MONAILabel server on Ubuntu, I connect to that IP on Mac. The connection is okay, but when I push on the Next Sample button, I get this error. The …

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## [Multi-GPU inference with MONAILabel](https://discourse.slicer.org/t/multi-gpu-inference-with-monailabel/37650)

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**Author:** [@xiang\_yao](https://discourse.slicer.org/u/xiang_yao)\
**Replies:** 3\
**Last updated:** [August 5, 2024, 10:03am UTC](https://discourse.slicer.org/t/multi-gpu-inference-with-monailabel/37650 "2024-08-05T10:03:40Z")

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May I ask if multi GPUs inference can be used in Windows or Linux systems? Currently, due to data size issues, it is evident that monailabel infers data in memory, i.e. CPU, without utilizing CUDA acceleration. If I hav…

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## [MonaiLabel CUDA out of memory with Bundle](https://discourse.slicer.org/t/monailabel-cuda-out-of-memory-with-bundle/29914)

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**Author:** [@FloCo](https://discourse.slicer.org/u/FloCo)\
**Replies:** 15\
**Last updated:** [August 1, 2024, 4:52am UTC](https://discourse.slicer.org/t/monailabel-cuda-out-of-memory-with-bundle/29914 "2024-08-01T04:52:49Z")

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Hello everyone, I am working with Slicer to do machine learning using MonaiLabel, the annotation and learning part work perfectly, it’s really nice tool ! Unfortunately I have troubles when I run the automatic segmenta…

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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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## [ MonaiLabel Models; Training from Scratch multiple times](https://discourse.slicer.org/t/monailabel-models-training-from-scratch-multiple-times/36988)

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**Author:** [@jessicasamir](https://discourse.slicer.org/u/jessicasamir)\
**Replies:** 0\
**Last updated:** [June 24, 2024, 6:26pm UTC](https://discourse.slicer.org/t/monailabel-models-training-from-scratch-multiple-times/36988 "2024-06-24T18:26:44Z")

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Hi everyone! I am a novice at 3D Slicer, but I am super excited to get started! I have already completed the tutorials MonaiLabel offers with the Radiology App and the MONAIBundle app which are both consistent with 3D S…

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## [Training and Validation Dice Values are 0](https://discourse.slicer.org/t/training-and-validation-dice-values-are-0/30689)

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**Author:** [@Dexter\_Luth](https://discourse.slicer.org/u/Dexter_Luth)\
**Replies:** 2\
**Last updated:** [June 6, 2024, 11:04am UTC](https://discourse.slicer.org/t/training-and-validation-dice-values-are-0/30689 "2024-06-06T11:04:17Z")

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Hi, When training a model all training and validation dice values are zero. configs segmentation module has been tailored to our needs by changing label titles and setting pretrained model loading to false. Here is som…

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## [Access MONAI Label server from 3D Slicer with authentication](https://discourse.slicer.org/t/access-monai-label-server-from-3d-slicer-with-authentication/36355)

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**Author:** [@vivit98](https://discourse.slicer.org/u/vivit98)\
**Replies:** 0\
**Last updated:** [May 23, 2024, 4:21pm UTC](https://discourse.slicer.org/t/access-monai-label-server-from-3d-slicer-with-authentication/36355 "2024-05-23T16:21:56Z")

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Hi, I am trying to access the MONAI Label app which is running on an external sever in OpenShift, while 3D Slicer is running locally. To my understanding, once the MONAI Label extension is installed, I should specify th…

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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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## [In the Monailabel plugin, there is no response when I press the "Submit Label" button](https://discourse.slicer.org/t/in-the-monailabel-plugin-there-is-no-response-when-i-press-the-submit-label-button/36046)

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**Author:** [@Prhat](https://discourse.slicer.org/u/Prhat)\
**Replies:** 0\
**Last updated:** [May 10, 2024, 5:15am UTC](https://discourse.slicer.org/t/in-the-monailabel-plugin-there-is-no-response-when-i-press-the-submit-label-button/36046 "2024-05-10T05:15:07Z")

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In the Monailabel plugin, there is no response when I press the “Submit Label” button

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## [Monai Label: accuracy not showing](https://discourse.slicer.org/t/monai-label-accuracy-not-showing/35957)

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**Author:** [@ILB](https://discourse.slicer.org/u/ILB)\
**Replies:** 1\
**Last updated:** [May 7, 2024, 9:05am UTC](https://discourse.slicer.org/t/monai-label-accuracy-not-showing/35957 "2024-05-07T09:05:56Z")

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Hi! I’m currently training a new model using Monai Label. I start using this configuration: monailabel start\_server --app apps/radiology --studies datasets/Task07\_Pancreas/imagesTr --conf models deepedit --conf use\_pr…

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