# Segmentation\_atlas\_template

**URL:** <https://discourse.slicer.org/t/segmentation-atlas-template/15780>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [February 1, 2021, 7:01pm UTC](https://discourse.slicer.org/t/segmentation-atlas-template/15780 "2021-02-01T19:01:23Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![sara\_sharifi](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sara_sharifi/32/9722_2.png) [@sara\_sharifi](https://discourse.slicer.org/u/sara_sharifi)\
**Post date:** [February 1, 2021, 7:01pm UTC](https://discourse.slicer.org/t/segmentation-atlas-template/15780/1 "2021-02-01T19:01:23Z")

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Operating system:7  
Slicer version:4.11  
Expected behavior:  
Actual behavior:  
Hi  
I am looking for a method called Template or Atlas method that I can use in 3D Slicer software or ITK Snap software to segment kidney images in CT scan . Please help me and introduce me to other software for segmenting CT images and its algorithms  
([sharifisara7373@gmail.com](mailto:sharifisara7373@gmail.com))  
Thank you

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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:** [February 2, 2021, 4:09am UTC](https://discourse.slicer.org/t/segmentation-atlas-template/15780/2 "2021-02-02T04:09:41Z")

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This documentation page is a good starting point for image segmentation: [Image Segmentation — 3D Slicer documentation](https://slicer.readthedocs.io/en/latest/user_guide/image_segmentation.html).

Nowadays classic atlas based methods are being replaced by neural networks. If you segment a few hundred images with manual/semi-automatic tools then you can use those to train a network that will segment similar images fully automatically (using for example [AIAA Segment Editor plugin](https://github.com/NVIDIA/ai-assisted-annotation-client/tree/master/slicer-plugin#nvidia-ai-assisted-annotation-aiaa-for-3d-slicer)). Check out [monai framework](https://monai.io/) for details and examples.

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**Author:** ![sara\_sharifi](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/sara_sharifi/32/9722_2.png) [@sara\_sharifi](https://discourse.slicer.org/u/sara_sharifi)\
**Post date:** [February 2, 2021, 5:41am UTC](https://discourse.slicer.org/t/segmentation-atlas-template/15780/3 "2021-02-02T05:41:33Z")

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thanks,  
Thanks, now I have reset the 3D slicer program by mistake and now I can’t find any module. I installed some items in the extension section, but it didn’t work and I only see the Event Broker module. How should I fix it?

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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:** [February 2, 2021, 1:50pm UTC](https://discourse.slicer.org/t/segmentation-atlas-template/15780/4 "2021-02-02T13:50:48Z")

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Probably you need to delete your [application settings](https://slicer.readthedocs.io/en/latest/user_guide/settings.html#settings-file-location). If you know which extension caused the trouble then let us know and we can have a look.