# Segmenting in a rotated volume

**URL:** <https://discourse.slicer.org/t/segmenting-in-a-rotated-volume/29147>\
**Category:** Support\
**Tags:** segmentation, transforms\
**Created:** [April 26, 2023, 5:23pm UTC](https://discourse.slicer.org/t/segmenting-in-a-rotated-volume/29147 "2023-04-26T17:23:14Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![chris\_nik](https://avatars.discourse-cdn.com/v4/letter/c/ac8455/32.png) [@chris\_nik](https://discourse.slicer.org/u/chris_nik)\
**Post date:** [April 26, 2023, 5:23pm UTC](https://discourse.slicer.org/t/segmenting-in-a-rotated-volume/29147/1 "2023-04-26T17:23:14Z")

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Hello dear community, it is me again. I made the following observation which induced a question:

Goal: to segment a rotated volume

Observation: if I create a new segment first and then rotate the volume in the ‘Transforms’ module, the segmentation tools work properly (s. Fig.1). However, if I rotate the volume first and then create a new segment, the area I mark with the segmentation tools gets distorted or is not completely filled (s. Fig.2). I then also get a notification that slice views orientation is not aligned with segmentation (s. Fig.3). I suppose this means that the orientation of the volume does not match the orientation of the segmentation. If I click on the latter notification button the volume gets rotated back to its original position, the segmentation tools work properly again, but my goal to segment in a rotated volume is not met anymore.

For this reason I normally create the segment first, then rotate the volume and it works fine for the most part. Sometimes the markup I create in one slice gets transferred to the adjacent one, however this behaviour is seldom. I also don’t get a notification that the slice orientation does not match the segmentation orientation. I still wanted to ask if I am doing it right and if there is an explanation for the behaviour in case of volume rotation and then segment creation.

Cheers

 ![Upload5](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/7/679b1295727d8d99aefb63e09b3586d42ecd11cc.png)  
Fig.1: Segment created, then volume rotated; proper fill of marked area

 ![Upload1](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/b/dbb41d6d48ab687e29a499b911fc0d7bc6389074.jpeg)  
 ![Upload2](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/8/b817ee79d9f9189ed742e79e93049c6dc336c1f4.jpeg)  
 ![Upload3](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/2/628fcbc58f20ba40206f893b07291c2d4c2972b1.jpeg)  
Fig.2: Volume rotated, then segment created; distortion and unproper fill of marked area, in the frontal view the brush tool seems to be unaligned with the marked area

 ![Upload4](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/2/1268b57a0a00a7712155ce05b21b203e1221ba65.jpeg)  
Fig.3: Notification that slice orientation is not aligned with segmentation in case of volume rotation and then segment creation

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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 26, 2023, 5:40pm UTC](https://discourse.slicer.org/t/segmenting-in-a-rotated-volume/29147/2 "2023-04-26T17:40:37Z")

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Interestingly, this topic [just came up](https://discourse.slicer.org/t/segmentation-using-paint-the-bulb-of-paint-disappears-after-the-image-is-oriented-in-accordance-with-the-anatomical-axes/29128) yesterday. There’s a [great description here](https://lassoan.github.io/SlicerSegmentationRecipes/ObliqueSliceSegmentation/). Maybe we can do something to make the behavior more intuitive.

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**Author:** ![chris\_nik](https://avatars.discourse-cdn.com/v4/letter/c/ac8455/32.png) [@chris\_nik](https://discourse.slicer.org/u/chris_nik)\
**Post date:** [April 26, 2023, 8:27pm UTC](https://discourse.slicer.org/t/segmenting-in-a-rotated-volume/29147/3 "2023-04-26T20:27:22Z")

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Thank you very much, I will try both methods : )