# Vertebra segmentation for volume masking

**URL:** <https://discourse.slicer.org/t/vertebra-segmentation-for-volume-masking/19143>\
**Category:** Support\
**Tags:** segmentation, spine\
**Created:** [August 10, 2021, 2:52pm UTC](https://discourse.slicer.org/t/vertebra-segmentation-for-volume-masking/19143 "2021-08-10T14:52:14Z")\
**Posts on this page:** 1\
**Showing post:** 4

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [August 10, 2021, 4:58pm UTC](https://discourse.slicer.org/t/vertebra-segmentation-for-volume-masking/19143/4 "2021-08-10T16:58:58Z")

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> [@ni5h](#):
>
> I use mri cron to visualise my annotation

What visualization mode is that you could not set up in Slicer?

> [@ni5h](#):
>
> i can only see the area, which I have annotated obviously, but what i need to see when I export is the whole series

You can save the whole image as well.

> [@ni5h](#):
>
> Therefore, can I mask the area above and below - would that export?

Yes, of course. You can have unlimited number of volumes, segmentations, segments in the scene and you can export all of them to files.

> [@ni5h](#):
>
> drawing each slice is time consuming and can imapct the rest of the series that I have annotated already

Slicer has many tools for spine segmentation.

For example, using classic tools, you can quickly segment the entire spinal column (each vertebra in a separate segment) using Grow from seeds effect, and filling internal holes using [this code snippet](https://gist.github.com/lassoan/0f45db8bae792ea19ccad36ceefbf52d).

There are also several fully automatic neural networks for spine segmentation. There is a pre-trained model for entire spine segmentation in [MONAILabel](https://github.com/Project-MONAI/MONAILabel#readme), but you can also train your own network for segmenting a single vertebra.

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