Segmenting in a rotated volume

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.


Fig.1: Segment created, then volume rotated; proper fill of marked area

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

Fig.3: Notification that slice orientation is not aligned with segmentation in case of volume rotation and then segment creation

Interestingly, this topic just came up yesterday. There’s a great description here. Maybe we can do something to make the behavior more intuitive.

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