# Segmenting CT scans taken by circular acquisition

**URL:** <https://discourse.slicer.org/t/segmenting-ct-scans-taken-by-circular-acquisition/43062>\
**Category:** Support\
**Created:** [May 23, 2025, 11:11am UTC](https://discourse.slicer.org/t/segmenting-ct-scans-taken-by-circular-acquisition/43062 "2025-05-23T11:11:12Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![sldamico131](https://avatars.discourse-cdn.com/v4/letter/s/e0b2c6/32.png) [@sldamico131](https://discourse.slicer.org/u/sldamico131)\
**Post date:** [May 23, 2025, 11:11am UTC](https://discourse.slicer.org/t/segmenting-ct-scans-taken-by-circular-acquisition/43062/1 "2025-05-23T11:11:12Z")

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Operating system: mac OS Sequoia  
Slicer version: 5.8.1  
I am trying to segment the ossicles in a seal skull. The CT scans were taken I believe using circular acquisition. When I load them into slicer, there are no slices. Instead, in the axial plane, I can just rotate the skull, and in the sagittal plane, the scans are mirrored. In the coronal plane is just a strange spiral. I can visualize the ossicles in the scans in the axial plane, but any attempt to segment them just leads to a large circle. Is there a way that I can segment these properly?

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [May 23, 2025, 3:04pm UTC](https://discourse.slicer.org/t/segmenting-ct-scans-taken-by-circular-acquisition/43062/2 "2025-05-23T15:04:47Z")

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Those are not the cross-sections, but the shadow image acquired at the detector. You will need the reconstructed cross-section images. Please read this to get familiar with CT

> <https://github.com/SlicerMorph/Tutorials/blob/main/microCT/README.md#what-is-microct-imaging>