# Issue with segmentation on non-axial volume

**URL:** <https://discourse.slicer.org/t/issue-with-segmentation-on-non-axial-volume/1021>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [September 8, 2017, 1:18pm UTC](https://discourse.slicer.org/t/issue-with-segmentation-on-non-axial-volume/1021 "2017-09-08T13:18:45Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![sleep\_research](https://avatars.discourse-cdn.com/v4/letter/s/b9e5f3/32.png) [@sleep\_research](https://discourse.slicer.org/u/sleep_research)\
**Post date:** [September 8, 2017, 1:18pm UTC](https://discourse.slicer.org/t/issue-with-segmentation-on-non-axial-volume/1021/1 "2017-09-08T13:18:45Z")

</div>

I have been trying to segment a series of MRI scans however when I use the paint tool to highlight a section on a single slice it seems to get split over neighbouring slices.  
I have attached a screenshot to help explain.

Would anyone please be able to help me figure out what is going on?

 ![Segmentation issue (1)](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/7/47f289fe1a28d2686e84349b28cbccdf71fb06e6.jpeg)

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [September 8, 2017, 1:29pm UTC](https://discourse.slicer.org/t/issue-with-segmentation-on-non-axial-volume/1021/2 "2017-09-08T13:29:34Z")

</div>

You have a non-axis-aligned volume. For slice-by-slice segmentation it may be easier to align slice views with the image plane as described in this topic:

> [@Display issue with RT structs and MR volume](https://discourse.slicer.org/t/display-issue-with-rt-structs-and-mr-volume/546/3):
>
> It seems that your MR volume axes are not aligned with patient anatomical axes. It’s not a problem, Slicer just shows slice viewers aligned with anatomical axes by default. Click “Rotate to volume plane” button in the slice view controller to align slice viewers to volume planes: [image] In the treatment planning software, did you draw contours with variable distance between them?

---

<div class="post-metadata">

**Author:** ![sleep\_research](https://avatars.discourse-cdn.com/v4/letter/s/b9e5f3/32.png) [@sleep\_research](https://discourse.slicer.org/u/sleep_research)\
**Post date:** [September 12, 2017, 1:57am UTC](https://discourse.slicer.org/t/issue-with-segmentation-on-non-axial-volume/1021/3 "2017-09-12T01:57:30Z")

</div>

Hi, thank you so much for this!! It seems to have solved our problem, I never realised that button was there to align the scans.

Thanks again, your help is greatly appreciated!