# CT perfusion coregistration to atlas

**URL:** <https://discourse.slicer.org/t/ct-perfusion-coregistration-to-atlas/42561>\
**Category:** Support\
**Tags:** registration, segmentation\
**Created:** [April 14, 2025, 4:51pm UTC](https://discourse.slicer.org/t/ct-perfusion-coregistration-to-atlas/42561 "2025-04-14T16:51:07Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![GioM](https://avatars.discourse-cdn.com/v4/letter/g/e56c9b/32.png) [@GioM](https://discourse.slicer.org/u/GioM)\
**Post date:** [April 14, 2025, 4:51pm UTC](https://discourse.slicer.org/t/ct-perfusion-coregistration-to-atlas/42561/1 "2025-04-14T16:51:07Z")

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Hi all,  
starting from the CT perfusion DICOM files I obtained the nifti penumbra VOI.  
Now I want to check which anatomical areas are affected based on the AAL atlas. I am stuck in the coregistration phase. How can I adapt a VOI extracted from a CT to an atlas?

Thanks for the advice, I am new to neuroimaging analysis, so any suggestions are welcome.

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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:** [April 14, 2025, 5:09pm UTC](https://discourse.slicer.org/t/ct-perfusion-coregistration-to-atlas/42561/2 "2025-04-14T17:09:20Z")

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You should be able to use any of the registration techniques to get a reasonable alignment.

> **[Registration — 3D Slicer documentation](https://slicer.readthedocs.io/en/latest/user_guide/registration.html)**

You may also want to see if SynthSeg can segment your CT directly.

> **[GitHub - BBillot/SynthSeg: Contrast-agnostic segmentation of MRI scans](https://github.com/BBillot/SynthSeg)**
>
> Contrast-agnostic segmentation of MRI scans

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<div class="post-metadata">

**Author:** ![GioM](https://avatars.discourse-cdn.com/v4/letter/g/e56c9b/32.png) [@GioM](https://discourse.slicer.org/u/GioM)\
**Post date:** [May 25, 2025, 8:40am UTC](https://discourse.slicer.org/t/ct-perfusion-coregistration-to-atlas/42561/3 "2025-05-25T08:40:34Z")

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Thanks. I first applied manual transformation to align the perfusion map to NCCT brain, then I used the same transformation for the segmented VOI (to align VOI to subject brain). And at last I run an affine registration of subject brain to a CT template and applied the same affine registration to the VOI (this last steps with antspyx script or with DSI Studio integrated tools). It works fine for my goal