# Segmentation for swine brain MRI

**URL:** <https://discourse.slicer.org/t/segmentation-for-swine-brain-mri/3861>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [August 21, 2018, 7:57pm UTC](https://discourse.slicer.org/t/segmentation-for-swine-brain-mri/3861 "2018-08-21T19:57:05Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![uchen9](https://avatars.discourse-cdn.com/v4/letter/u/b4bc9f/32.png) [@uchen9](https://discourse.slicer.org/u/uchen9)\
**Post date:** [August 21, 2018, 7:57pm UTC](https://discourse.slicer.org/t/segmentation-for-swine-brain-mri/3861/1 "2018-08-21T19:57:05Z")

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Operating system: Windows  
Slicer version: 4.8.1

Hello,  
I require a segmentation of part of a swine brain and I have an atlas to use; however the EMSegmenter with Atlas does not allow for the swine atlas to be selected as the “task”. I am very new to segmentation- is there another module I can use to segment a volume using my Atlas or is there some way to upload my atlas as the task?

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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 21, 2018, 9:05pm UTC](https://discourse.slicer.org/t/segmentation-for-swine-brain-mri/3861/2 "2018-08-21T21:05:58Z")

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If you have a single pair of grayscale image + segmentation as atlas, then you can use image registration to warp the atlas to the new case:

- install Elastix extension
- register grayscale volumes using “General registration (Elastix)” module (atlas grayscale volume is moving, new case grayscale volume is fixed volume; choose to save the computed transform)
- apply the computed transform to the atlas segmentation to warp it to the new case

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<div class="post-metadata">

**Author:** ![uchen9](https://avatars.discourse-cdn.com/v4/letter/u/b4bc9f/32.png) [@uchen9](https://discourse.slicer.org/u/uchen9)\
**Post date:** [August 22, 2018, 3:19pm UTC](https://discourse.slicer.org/t/segmentation-for-swine-brain-mri/3861/3 "2018-08-22T15:19:14Z")

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Thank you, I will try this out. However, I also have another question- what is the best method/a good tutorial for segmenting the atlas in the first place? I have been trying to use the paint tool in Segment Editor but what I am painting is not showing on the atlas or creating an output volume.

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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 22, 2018, 3:21pm UTC](https://discourse.slicer.org/t/segmentation-for-swine-brain-mri/3861/4 "2018-08-22T15:21:50Z")

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This is a good starting point for learning segmentation: [https://www.slicer.org/wiki/Documentation/Nightly/Training#Slicer4\_Image\_Segmentation](https://www.slicer.org/wiki/Documentation/Nightly/Training#Slicer4_Image_Segmentation)