# Segmentation for MRI rat brains

**URL:** <https://discourse.slicer.org/t/segmentation-for-mri-rat-brains/3390>\
**Category:** Support\
**Created:** [July 5, 2018, 4:34pm UTC](https://discourse.slicer.org/t/segmentation-for-mri-rat-brains/3390 "2018-07-05T16:34:38Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![alaleh\_alivar](https://avatars.discourse-cdn.com/v4/letter/a/e36b37/32.png) [@alaleh\_alivar](https://discourse.slicer.org/u/alaleh_alivar)\
**Post date:** [July 5, 2018, 4:34pm UTC](https://discourse.slicer.org/t/segmentation-for-mri-rat-brains/3390/1 "2018-07-05T16:34:38Z")

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Slicer version: 4.9.0

I want to upload an external atlas named as WHS\_SD\_rat\_atlas\_v2 for using it as a reference for brain segmentation. But when I use Em segment with atlas, there is no task defined for this purpose. When I want to create new task, there is error loading in the software. My question is how can I use this external atlas in 3D slicer for rat brain segmentation? ( All the documents are for versions 3.6)

Thanks for your help.

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [July 19, 2018, 2:06pm UTC](https://discourse.slicer.org/t/segmentation-for-mri-rat-brains/3390/2 "2018-07-19T14:06:07Z")

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Unfortunately the EMSegmenter isn’t getting much support these days so maybe only the basics are working - we may remove it from the distribution soon. You can have a look at some previous discussion that may help (like using Slicer3, but be forewarned that it’s not maintained either).

[https://discourse.slicer.org/tags/emsegmenter](https://discourse.slicer.org/tags/emsegmenter)