# Non rigid registration of brain

**URL:** <https://discourse.slicer.org/t/non-rigid-registration-of-brain/5360>\
**Category:** Support\
**Created:** [January 14, 2019, 3:21pm UTC](https://discourse.slicer.org/t/non-rigid-registration-of-brain/5360 "2019-01-14T15:21:59Z")\
**Posts on this page:** 8\
**Page:** 1

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**Author:** ![RadioQuest](https://avatars.discourse-cdn.com/v4/letter/r/85f322/32.png) [@RadioQuest](https://discourse.slicer.org/u/RadioQuest)\
**Post date:** [January 14, 2019, 3:21pm UTC](https://discourse.slicer.org/t/non-rigid-registration-of-brain/5360/1 "2019-01-14T15:21:59Z")

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Hi…  
I want to register post surgical brain MRI images to presurgical baseline scan. Can someone please provide me with the links to tutorial or guidance as how to achieve this in most reliable way?  
Thanks

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**Author:** ![spujol](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/spujol/32/3498_2.png) [@spujol](https://discourse.slicer.org/u/spujol)\
**Post date:** [January 14, 2019, 7:03pm UTC](https://discourse.slicer.org/t/non-rigid-registration-of-brain/5360/2 "2019-01-14T19:03:24Z")

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Hello,

The Slicer registration tutorial shows the basics of rigid and non-rigid registration using BRAINS:  
[https://www.slicer.org/wiki/Documentation/4.8/Training#Slicer4\_Image\_Registration](https://www.slicer.org/wiki/Documentation/4.8/Training#Slicer4_Image_Registration)

The Registration Case library provides examples of registration strategies for brain tumor and TBI follow-up:  
[https://www.na-mic.org/wiki/Projects:RegistrationDocumentation:UseCaseInventory:BrainIntraMRI](https://www.na-mic.org/wiki/Projects:RegistrationDocumentation:UseCaseInventory:BrainIntraMRI)

Sonia

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**Author:** ![RadioQuest](https://avatars.discourse-cdn.com/v4/letter/r/85f322/32.png) [@RadioQuest](https://discourse.slicer.org/u/RadioQuest)\
**Post date:** [January 15, 2019, 9:56am UTC](https://discourse.slicer.org/t/non-rigid-registration-of-brain/5360/3 "2019-01-15T09:56:15Z")

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Thank you very much. I had checked basic tutorial but needed help with customization of settings.  
I will try it now,  
Kind Regards,  
RQ

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**Author:** ![RadioQuest](https://avatars.discourse-cdn.com/v4/letter/r/85f322/32.png) [@RadioQuest](https://discourse.slicer.org/u/RadioQuest)\
**Post date:** [January 16, 2019, 3:26pm UTC](https://discourse.slicer.org/t/non-rigid-registration-of-brain/5360/4 "2019-01-16T15:26:59Z")

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Hi. I tried to work as per [https://www.na-mic.org/wiki/Projects:RegistrationLibrary:RegLib\_C37](https://www.na-mic.org/wiki/Projects:RegistrationLibrary:RegLib_C37)  
However, I am new to the slicer. I am unable to execute registration as I need more help with setting, selection of volume etc. is there any video for the whole tutorial with details of modules and stepwise instructions.  
(eg which volume to use in step3 ?)  
Thanks

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**Author:** ![spujol](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/spujol/32/3498_2.png) [@spujol](https://discourse.slicer.org/u/spujol)\
**Post date:** [January 18, 2019, 5:38pm UTC](https://discourse.slicer.org/t/non-rigid-registration-of-brain/5360/5 "2019-01-18T17:38:35Z")

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The video tutorial below shows the steps for case #37:

[https://spujol.github.io/3DSlicerTutorial-Registration/](https://spujol.github.io/3DSlicerTutorial-Registration/)

Sonia

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<div class="post-metadata">

**Author:** ![RadioQuest](https://avatars.discourse-cdn.com/v4/letter/r/85f322/32.png) [@RadioQuest](https://discourse.slicer.org/u/RadioQuest)\
**Post date:** [January 21, 2019, 11:26am UTC](https://discourse.slicer.org/t/non-rigid-registration-of-brain/5360/6 "2019-01-21T11:26:24Z")

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Dear Sonia  
Thank you very much. This is very useful.  
Kind Regards,  
RQ

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**Author:** ![RadioQuest](https://avatars.discourse-cdn.com/v4/letter/r/85f322/32.png) [@RadioQuest](https://discourse.slicer.org/u/RadioQuest)\
**Post date:** [January 22, 2019, 4:51pm UTC](https://discourse.slicer.org/t/non-rigid-registration-of-brain/5360/7 "2019-01-22T16:51:13Z")

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Dear Sonia,  
I have performed registration as per this tutorial.  
Could you please tell me what are the criteria to determine if my registration is accurate despite brain deformation?  
is there any publication to support this methodology? I need to validate my results.  
Thanks.  
Kind Regards,  
RQ

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**Author:** ![spujol](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/spujol/32/3498_2.png) [@spujol](https://discourse.slicer.org/u/spujol)\
**Post date:** [January 23, 2019, 1:54pm UTC](https://discourse.slicer.org/t/non-rigid-registration-of-brain/5360/8 "2019-01-23T13:54:03Z")

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A simple approach is to use a dense set of anatomical landmarks.  
The General Registration module is based on the BRAINS library:  
_BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit, Johnson H.J., Harris G., Williams K., The Insight Journal, 2007.([http://hdl.handle.net/1926/1291](http://hdl.handle.net/1926/1291))_

> **[BRAINSTools/BRAINSFit at main · BRAINSia/BRAINSTools](https://github.com/BRAINSia/BRAINSTools/tree/main/BRAINSFit)**
>
> main/BRAINSFit