# Using MONAILabel for vertebrae segmentation

**URL:** <https://discourse.slicer.org/t/using-monailabel-for-vertebrae-segmentation/27511>\
**Category:** Support\
**Tags:** monailabel\
**Created:** [January 28, 2023, 12:58am UTC](https://discourse.slicer.org/t/using-monailabel-for-vertebrae-segmentation/27511 "2023-01-28T00:58:19Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![DeepaKrishnaswamy](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/deepakrishnaswamy/32/8913_2.png) [@DeepaKrishnaswamy](https://discourse.slicer.org/u/DeepaKrishnaswamy)\
**Post date:** [January 28, 2023, 12:58am UTC](https://discourse.slicer.org/t/using-monailabel-for-vertebrae-segmentation/27511/1 "2023-01-28T00:58:19Z")

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Hi,

I’m trying to perform inference using the pretrained model from the 3 stage vertebrae segmentation pipeline from MONAI Label, but have been running into a few issues on a Windows machine with Slicer version 5.2.1:

1. I’ve been able to start the server and run the first step localization\_spine without runtime errors, but unfortunately it produces empty segments. I’ve tried this using a nifti file from both Verse2019 and Verse2020, which are the datasets the 3 stage pipeline were originally trained on. I’ve tried other models such as the segmentation\_spleen and the segmentation\_full\_ct from here:[radiology\_full\_ct-upgraded-HYBRID - Google Drive](https://drive.google.com/drive/folders/17eJan-8_oNCnZyJk8B9zLQpwaOjtDuKi?usp=share_link), and those have produced mostly accurate output labels.

2. I also tried running the entire vertebrae\_pipeline, but this resulted in the following error:  

Has anyone encountered similar issues? Thanks!

Deepa

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**Author:** ![mau\_igna\_06](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mau_igna_06/32/9056_2.png) [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Post date:** [January 28, 2023, 1:03pm UTC](https://discourse.slicer.org/t/using-monailabel-for-vertebrae-segmentation/27511/2 "2023-01-28T13:03:38Z")

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> [@DeepaKrishnaswamy](#):
>
> Has anyone encountered similar issues?

Hi. Yes. I couldn’t make it work either

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**Author:** ![diazandr3s](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/diazandr3s/32/9973_2.png) [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)\
**Post date:** [January 30, 2023, 7:36pm UTC](https://discourse.slicer.org/t/using-monailabel-for-vertebrae-segmentation/27511/3 "2023-01-30T19:36:35Z")

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Hi @DeepaKrishnaswamy,

Thanks for providing the details of your experience using MONAI Label here and on the issue here: [vertebrae\_pipeline produces an error during inference · Issue #1268 · Project-MONAI/MONAILabel · GitHub](https://github.com/Project-MONAI/MONAILabel/issues/1268#issuecomment-1409022013)

It is good that you managed to run the vertebra model on the Medical Segmentation Decathlon dataset.

The vertebra segmentation model was trained only on a portion of the VerSe dataset (~60 volumes). I’ve also had similar issues with that dataset and I think it was because some files were corrupted or had wrong NIfTI headers.

If you have a GPU, you could also try the whole-body CT segmentation model available here: [radiology\_full\_ct-upgraded-HYBRID - Google Drive](https://drive.google.com/drive/folders/17eJan-8_oNCnZyJk8B9zLQpwaOjtDuKi?usp=share_link)

That model also segments all vertebras.

Thanks again!

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<div class="post-metadata">

**Author:** ![diazandr3s](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/diazandr3s/32/9973_2.png) [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)\
**Post date:** [January 30, 2023, 7:42pm UTC](https://discourse.slicer.org/t/using-monailabel-for-vertebrae-segmentation/27511/4 "2023-01-30T19:42:53Z")

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Hi @mau_igna_06,

Is it the same error you faced last time?  
As far as I remember the issue you faced was related to not having computing resources. Did you manage to run these models on a bigger GPU/CPU?  
If you’re facing a different issue, please don’t hesitate to post the logs directly on the MONAI Label repository: [Issues · Project-MONAI/MONAILabel · GitHub](https://github.com/Project-MONAI/MONAILabel/issues)

Thanks!