# Segmentation MRI rat

**URL:** <https://discourse.slicer.org/t/segmentation-mri-rat/16485>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [March 12, 2021, 3:18am UTC](https://discourse.slicer.org/t/segmentation-mri-rat/16485 "2021-03-12T03:18:04Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![gloria](https://avatars.discourse-cdn.com/v4/letter/g/b38774/32.png) [@gloria](https://discourse.slicer.org/u/gloria)\
**Post date:** [March 12, 2021, 3:18am UTC](https://discourse.slicer.org/t/segmentation-mri-rat/16485/1 "2021-03-12T03:18:04Z")

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Hi

I want to know if for the segmentation of gray and white matter of a rat mri I need an atlas or not???

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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:** [April 14, 2021, 4:38am UTC](https://discourse.slicer.org/t/segmentation-mri-rat/16485/2 "2021-04-14T04:38:38Z")

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Considering there was not response, most likely Slicer users don’t segment rat MRI using an atlas.

You can probably get good segmentation by using a few modules:

- Make the image more uniform using bias correction by “N4ITK MRI Bias Correction” module
- Apply anisotropic smoothing to reduce noise by “Curvature anisotropic diffusion” or “Gradient anisotropic diffusion” module
- Use SwissSkullStripper extension to extract the brain (choose a similar existing rat MRI image and corresponding brain mask as inputs)
- Segment white and gray matter using Segment Editor (Thresholding effect, followed by Smoothing effect, using Joint smoothing method)