Problem with segmentation of MCA territory on axial view


I think I have a similar problem to what described in this post
but I don’t understand how to use Crop Volume to solve the issue.

My aim is to mark the 3D territory of the middle cerebral artery on CT angiography scans. In order to do so I am using some axial reference pictures:

Therefore I would like to tilt my scans to display them in the same view as the reference images (at the same tilting angle which is good for recognising the MCA territory on the axial view), so that I could mark the MCA territory by simply “imitating” what is displayed on the reference. Then I would like to use “fill in between slices” to obtain the 3D vascular territory and refine manually with the erase tool or further drawing where required.

The problem is that if I rotate my volume and then use the draw tool in segment editor I get the artifacts described in other posts:


And I have tried to use the Crop Volume module but I don’t see any difference, the artifacts are still there. Or maybe I didn’t understand what I’m supposed to do in Crop Volume. Can you help?

Thank you

I think I have actually solved my problem thanks to the reply to this post.
Now I first create a ROI, rotate my volume but not the ROI and then crop so the new cropped volume is aligned to the slicer axis and the segmentation tools work fine.

Sorry for my first post, that was really easy in the end.

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interesting and usful

We’ve added a button to Segment editor that appears when slices are misaligned and clicking that automatically aligns them to the segmentation (available in nightly builds from tomorrow).

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