# Head CT MRI fusion/registration

**URL:** <https://discourse.slicer.org/t/head-ct-mri-fusion-registration/1333>\
**Category:** Support\
**Tags:** registration\
**Created:** [October 31, 2017, 3:13pm UTC](https://discourse.slicer.org/t/head-ct-mri-fusion-registration/1333 "2017-10-31T15:13:48Z")\
**Posts on this page:** 7\
**Page:** 2

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**Author:** ![Saima](https://avatars.discourse-cdn.com/v4/letter/s/9d8465/32.png) [@Saima](https://discourse.slicer.org/u/Saima)\
**Post date:** [October 23, 2019, 5:30am UTC](https://discourse.slicer.org/t/head-ct-mri-fusion-registration/1333/22 "2019-10-23T05:30:01Z")

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Hi Andras,  
swiss skull stripper not giving good results. some portion of the brain is missed by it. what can I use instead of this or is there a way to change the parameters of the algorithm it is using

thanks

regards,  
Saima Safdar

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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:** [October 23, 2019, 1:33pm UTC](https://discourse.slicer.org/t/head-ct-mri-fusion-registration/1333/23 "2019-10-23T13:33:31Z")

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You can create your own atlas and mask image that better represents your patient population.

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**Author:** ![mubafz](https://avatars.discourse-cdn.com/v4/letter/m/e9a140/32.png) [@mubafz](https://discourse.slicer.org/u/mubafz)\
**Post date:** [June 24, 2021, 3:51pm UTC](https://discourse.slicer.org/t/head-ct-mri-fusion-registration/1333/24 "2021-06-24T15:51:49Z")

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Hi Amir,

Did you end up working out whats the best way in Slicer for pre-implant MRI/Post-op for precise registration.

I am just browsing through looking for info on this and came across this three year old thread.

Regards,  
M

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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:** [June 25, 2021, 10:01pm UTC](https://discourse.slicer.org/t/head-ct-mri-fusion-registration/1333/25 "2021-06-25T22:01:51Z")

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Many things have changed in the past 2-3 years. Therefore, instead of reviving an old thread, it may be better to start a new one. Describe your high-level goal, the specific problem you have, and provide images (at least screenshots).

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**Author:** ![Ella1](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ella1/32/15590_2.png) [@Ella1](https://discourse.slicer.org/u/Ella1)\
**Post date:** [August 25, 2022, 7:31pm UTC](https://discourse.slicer.org/t/head-ct-mri-fusion-registration/1333/26 "2022-08-25T19:31:11Z")

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This link is not active anymore.  
I mean when I click on any file in the download section, Error 404 has appeared.  
Would you provide another link?  
Thanks

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**Author:** ![Atefeh.Zeinoddini](https://avatars.discourse-cdn.com/v4/letter/a/bbe5ce/32.png) [@Atefeh.Zeinoddini](https://discourse.slicer.org/u/Atefeh.Zeinoddini)\
**Post date:** [May 7, 2025, 12:56am UTC](https://discourse.slicer.org/t/head-ct-mri-fusion-registration/1333/27 "2025-05-07T00:56:38Z")

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Hi, Do you have suggestion for robust registration of CT and MRI? I am looking for a preferably free software, do you have recommendations? many thanks

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**Author:** ![mikebind](https://avatars.discourse-cdn.com/v4/letter/m/71e660/32.png) [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Post date:** [May 7, 2025, 5:06pm UTC](https://discourse.slicer.org/t/head-ct-mri-fusion-registration/1333/28 "2025-05-07T17:06:35Z")

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In my experience [ANTs](https://github.com/ANTsX/ANTs) works very well for this, and is available in Slicer through the extension [SlicerANTs](https://github.com/netstim/SlicerANTs). It has many settings for deformable registration, but if you just want to do rigid registration, the “Rigid” preset works well. You will need to read enough to understand and make a selection in the Initial Moving Transform section and understand Slicer enough to apply the resulting transform or view the generated transformed image volume.

[Previous page](https://discourse.slicer.org/t/head-ct-mri-fusion-registration/1333.md?page=1)