# \#monai

**URL:** https://discourse.slicer.org/tag/monai/426.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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## [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 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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## [Contribution to the SlicerMONAIAuto3DSeg extension](https://discourse.slicer.org/t/contribution-to-the-slicermonaiauto3dseg-extension/34739)

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**Author:** [@rfenioux](https://discourse.slicer.org/u/rfenioux)\
**Replies:** 5\
**Last updated:** [April 7, 2025, 7:57am UTC](https://discourse.slicer.org/t/contribution-to-the-slicermonaiauto3dseg-extension/34739 "2025-04-07T07:57:33Z")

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There has been an internal effort at Kitware Europe to simplify the use of segmentation models available as MONAI bundles from 3D Slicer. The goal of this post is to gather some feedback about the best way to share this…

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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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## [Matching Monai orientation with "arrayFromVolume" output](https://discourse.slicer.org/t/matching-monai-orientation-with-arrayfromvolume-output/37810)

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**Author:** [@chbricout](https://discourse.slicer.org/u/chbricout)\
**Replies:** 1\
**Last updated:** [August 11, 2024, 9:32pm UTC](https://discourse.slicer.org/t/matching-monai-orientation-with-arrayfromvolume-output/37810 "2024-08-11T21:32:51Z")

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Hi everyone, I’m developing a simple extension to integrate a motion estimation model into Slicer. I’m using MONAI for most of the training, including data loading. However, I’ve noticed that the volume I get when using…

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## [Convert Monai bundle to torch file for SlicerMONAIAuto3DSeg](https://discourse.slicer.org/t/convert-monai-bundle-to-torch-file-for-slicermonaiauto3dseg/34836)

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**Author:** [@slava](https://discourse.slicer.org/u/slava)\
**Replies:** 9\
**Last updated:** [July 10, 2024, 9:44pm UTC](https://discourse.slicer.org/t/convert-monai-bundle-to-torch-file-for-slicermonaiauto3dseg/34836 "2024-07-10T21:44:32Z")

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Hi, I am trying to use my network trained using Monai Auto3Dseg in the SlicerMONAIAuto3DSeg plugin. SlicerMONAIAuto3DSeg imports the torch file with a list including config information and the network weights. Monai out…

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## [MONAI Project Resources for Mandible Image Segmentation](https://discourse.slicer.org/t/monai-project-resources-for-mandible-image-segmentation/36127)

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**Author:** [@Havay](https://discourse.slicer.org/u/Havay)\
**Replies:** 6\
**Last updated:** [June 6, 2024, 7:58pm UTC](https://discourse.slicer.org/t/monai-project-resources-for-mandible-image-segmentation/36127 "2024-06-06T19:58:42Z")

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Hello, we are a medical research team from Duke & JHU, currently working on image segmentation tasks for damaged mandibles. I have reviewed your MONAI project, and I am impressed by the results. I would like to inquire i…

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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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## [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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## [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…

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## [Monai auto3dsegmenta - error from python package information](https://discourse.slicer.org/t/monai-auto3dsegmenta-error-from-python-package-information/35693)

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**Author:** [@eNable\_Polska](https://discourse.slicer.org/u/eNable_Polska)\
**Replies:** 1\
**Last updated:** [April 24, 2024, 1:13am UTC](https://discourse.slicer.org/t/monai-auto3dsegmenta-error-from-python-package-information/35693 "2024-04-24T01:13:42Z")

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I cannot run the Monai Auto3dseg module. Python package information gives me the following information: Traceback (most recent call last): File "C:\\Users\\krzys\\AppData\\Local\\slicer.org\\Slicer 5.6.2\\bin\\Python\\slicer\\u…

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## [ImageAugmenter extension released!](https://discourse.slicer.org/t/imageaugmenter-extension-released/35690)

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**Author:** [@ciro.raggio](https://discourse.slicer.org/u/ciro.raggio)\
**Replies:** 0\
**Last updated:** [April 23, 2024, 5:54pm UTC](https://discourse.slicer.org/t/imageaugmenter-extension-released/35690 "2024-04-23T17:54:22Z")

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We are happy to announce that the ImageAugmenter extension is now available in the preview release of 3D Slicer. This new extension lets you easily augment your medical image datasets without writing a single line of cod…

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## [Training on MONAILabel without GPU](https://discourse.slicer.org/t/training-on-monailabel-without-gpu/33320)

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**Author:** [@Vineet\_Saravanan](https://discourse.slicer.org/u/Vineet_Saravanan)\
**Replies:** 0\
**Last updated:** [December 10, 2023, 12:36am UTC](https://discourse.slicer.org/t/training-on-monailabel-without-gpu/33320 "2023-12-10T00:36:30Z")

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Hello. I am trying to train with MONAILabel for artery segmentation. I don’t have a GPU on my laptop, and I am getting an error here: How/where would I change it to map the storage to my CPU? I do have an integrated …

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## [MRI Fat segmentation](https://discourse.slicer.org/t/mri-fat-segmentation/29735)

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**Author:** [@Spiros\_Karkavitsas](https://discourse.slicer.org/u/Spiros_Karkavitsas)\
**Replies:** 0\
**Last updated:** [May 30, 2023, 7:44pm UTC](https://discourse.slicer.org/t/mri-fat-segmentation/29735 "2023-05-30T19:44:00Z")

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Hello Currently, I am trying to segment the adipose tissue from MR Images. Now I am using the radiology app from MONAILabel. I am manually segment the data using Slicer (see attached). I do not need to accurately segme…

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## [MONAI events before Project Week](https://discourse.slicer.org/t/monai-events-before-project-week/27276)

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**Author:** [@pieper](https://discourse.slicer.org/u/pieper)\
**Replies:** 12\
**Last updated:** [January 28, 2023, 6:43pm UTC](https://discourse.slicer.org/t/monai-events-before-project-week/27276 "2023-01-28T18:43:44Z")

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As we’ve done as part of the previous two times we are going to hold a 2-hour workshop on the use of MONAI Label in 3D Slicer the week before Project Week. This will include updates from several people in the NA-MIC comm…

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## [MONAI - Local Project "Tree" and Configuration - Results](https://discourse.slicer.org/t/monai-local-project-tree-and-configuration-results/26664)

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**Author:** [@dalv.silvermann](https://discourse.slicer.org/u/dalv.silvermann)\
**Replies:** 1\
**Last updated:** [December 12, 2022, 1:37pm UTC](https://discourse.slicer.org/t/monai-local-project-tree-and-configuration-results/26664 "2022-12-12T13:37:44Z")

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Dear colleagues, I have a question about the results of MONAI Label Service which I’m using on my tower-server with Asus Nvidia GeForce RTX 3080 10GiB based on Windows Server 2019 OS. We are testing two project struct…

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## [Monai label. CUDA out of memory](https://discourse.slicer.org/t/monai-label-cuda-out-of-memory/26161)

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**Author:** [@dalv.silvermann](https://discourse.slicer.org/u/dalv.silvermann)\
**Replies:** 6\
**Last updated:** [December 8, 2022, 5:13pm UTC](https://discourse.slicer.org/t/monai-label-cuda-out-of-memory/26161 "2022-12-08T17:13:24Z")

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I have a question about Monai Label. Maybe somebody has faced the similar problem. I use deepedit from radiology app without any global code changes on my tower-server with Asus Nvidia GeForce RTX 3080 10GiB. I try t…

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## [GTC Keynote MONAI and Slicer](https://discourse.slicer.org/t/gtc-keynote-monai-and-slicer/22653)

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**Author:** [@pieper](https://discourse.slicer.org/u/pieper)\
**Replies:** 5\
**Last updated:** [September 22, 2022, 1:23pm UTC](https://discourse.slicer.org/t/gtc-keynote-monai-and-slicer/22653 "2022-09-22T13:23:55Z")

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Congrats to the MONAILabel team for getting a spot in the Nvidia keynote and getting some screen time for Slicer on the big stage :+1: The whole keynote is on youtube, and this link takes you directly to the part about…

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## [Why not working monai pathology?](https://discourse.slicer.org/t/why-not-working-monai-pathology/24703)

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**Author:** [@jhchoi](https://discourse.slicer.org/u/jhchoi)\
**Replies:** 1\
**Last updated:** [August 10, 2022, 1:48pm UTC](https://discourse.slicer.org/t/why-not-working-monai-pathology/24703 "2022-08-10T13:48:39Z")

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I installed monai to 3d slicer 5.0. It was working very well(as using radiology with sample files). so I want to change from radiology to pathology and other sample files. but in this pic, it was not working… how to …

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## [Unexpected results from training new model in Monai Label](https://discourse.slicer.org/t/unexpected-results-from-training-new-model-in-monai-label/24681)

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**Author:** [@mahranahm](https://discourse.slicer.org/u/mahranahm)\
**Replies:** 8\
**Last updated:** [August 9, 2022, 2:28pm UTC](https://discourse.slicer.org/t/unexpected-results-from-training-new-model-in-monai-label/24681 "2022-08-09T14:28:59Z")

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Hi 3D slicer community, We are working to train a new model to segment the heart. We have 6 pre-labelled scans which I am using for the initial training. I kept all the parameters on default except increasing the max\_ep…

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## [MONAI Label - unable to get the target\_spacing and spatial\_size using heuristic\_planner](https://discourse.slicer.org/t/monai-label-unable-to-get-the-target-spacing-and-spatial-size-using-heuristic-planner/24391)

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**Author:** [@hourglassnam](https://discourse.slicer.org/u/hourglassnam)\
**Replies:** 4\
**Last updated:** [July 19, 2022, 10:38pm UTC](https://discourse.slicer.org/t/monai-label-unable-to-get-the-target-spacing-and-spatial-size-using-heuristic-planner/24391 "2022-07-19T22:38:47Z")

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Dear Slicer community, I have a few minor questions and one big question on MONAI Label as I try to train from scratch. So let me start by stating the big question first. Because I do not know the target\_spacing and s…

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## [Is there anyway to use MONAI LABEL on a Macbook?](https://discourse.slicer.org/t/is-there-anyway-to-use-monai-label-on-a-macbook/23921)

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**Author:** [@Celina\_Hallal](https://discourse.slicer.org/u/Celina_Hallal)\
**Replies:** 7\
**Last updated:** [June 19, 2022, 9:29pm UTC](https://discourse.slicer.org/t/is-there-anyway-to-use-monai-label-on-a-macbook/23921 "2022-06-19T21:29:19Z")

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Operating system: MacOS Monterey Slicer version: latest version (5.0) Python version: 3.10.5 I’m a totally newbie, so my questions may sound a little dumb. Is there anyway to use MONAI LABEL on a Mac M1? Probably will…

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## [Monai server launch failing](https://discourse.slicer.org/t/monai-server-launch-failing/23757)

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**Author:** [@Nayra\_Pumar](https://discourse.slicer.org/u/Nayra_Pumar)\
**Replies:** 8\
**Last updated:** [June 10, 2022, 1:49pm UTC](https://discourse.slicer.org/t/monai-server-launch-failing/23757 "2022-06-10T13:49:39Z")

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I’ve cloned the MONAIlabel github repository (GitHub - Project-MONAI/MONAILabel: MONAI Label is an intelligent open source image labeling and learning tool.), set up a python 3.9 python environment, installed cuda and th…

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## [MONAILABEL optimization](https://discourse.slicer.org/t/monailabel-optimization/22678)

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**Author:** [@Mahdis\_Khodadadi](https://discourse.slicer.org/u/Mahdis_Khodadadi)\
**Replies:** 4\
**Last updated:** [April 11, 2022, 9:32pm UTC](https://discourse.slicer.org/t/monailabel-optimization/22678 "2022-04-11T21:32:03Z")

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Hello everyone, I am working on pelvic bone segmentation in CT scans using MONAILABEL and 3D Slicer. I used the “deepedit” app and trained the network using 8 perfect manually segmented mask files and got 82% accuracy.…

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## [MONAILABEL plugin | pelvis segmentation in MRI](https://discourse.slicer.org/t/monailabel-plugin-pelvis-segmentation-in-mri/22283)

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**Author:** [@Mahdis\_Khodadadi](https://discourse.slicer.org/u/Mahdis_Khodadadi)\
**Replies:** 8\
**Last updated:** [March 24, 2022, 8:40pm UTC](https://discourse.slicer.org/t/monailabel-plugin-pelvis-segmentation-in-mri/22283 "2022-03-24T20:40:29Z")

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Operating system: Windows 10 Slicer version: latest version I want to segment pelvic in MRI from the SMIR dataset using the MONAILABEL plugin. I have read relatively a lot about this plugin. However, I can’t perform th…

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## [Monai/monailabel training from scratch](https://discourse.slicer.org/t/monai-monailabel-training-from-scratch/19676)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 1\
**Last updated:** [September 15, 2021, 12:28am UTC](https://discourse.slicer.org/t/monai-monailabel-training-from-scratch/19676 "2021-09-15T00:28:00Z")

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We would like to try Monai/MonaiLabel to segment mouse fetuses which are scanned via contrast-enhanced microCT . I don’t think any of the existing models will be relevant for us. How does one go developing a model from s…