# How to align brain CT and MR images？

**URL:** https://discourse.slicer.org/t/how-to-align-brain-ct-and-mr-images/22080
**Category:** Support
**Tags:** registration
**Created:** [February 21, 2022, 4:42am UTC](https://discourse.slicer.org/t/how-to-align-brain-ct-and-mr-images/22080 "2022-02-21T04:42:07Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![yllgl](https://avatars.discourse-cdn.com/v4/letter/y/8e7dd6/32.png) [@yllgl](https://discourse.slicer.org/u/yllgl)
#### Post date: [February 21, 2022, 4:42am UTC](https://discourse.slicer.org/t/how-to-align-brain-ct-and-mr-images/22080/1 "2022-02-21T04:42:07Z")

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I have tried brain rigid image base registration in slicer3d. But the result is not very good. Could any body give my some suggestions about how to register the brain CT and MR image? I don’t want to use landmark method, because I want to do it automatically using python code.  
here is my data.[download](https://icedrive.net/s/iF8j9w46ZCNw1ZxD2BZR5NRu3B5a)  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/a/4/a4f9c82b6d082e5453aed1b9ac27e56be698145d.png)

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### Author: ![simonoxen](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/simonoxen/32/66398_2.png) [@simonoxen](https://discourse.slicer.org/u/simonoxen)
#### Post date: [February 21, 2022, 6:36pm UTC](https://discourse.slicer.org/t/how-to-align-brain-ct-and-mr-images/22080/2 "2022-02-21T18:36:32Z")

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Hi, I just run a rigid registration with SlicerANTs and got a good result. You can probably achieve the same with SlicerElastix.

 ![Screenshot 2022-02-21 at 19.30.00](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/5/45c54d071e72c7ba3c6a863887d010cc950a7cf2.jpeg)

You can see the ants command in the slicer log and then run the antsRegistrationCLI module from python. Alternatively, you can the see the test in General Registration (ANTs) to see how to run it’s logic.