# Segmentation problem with MRI (geometric issues)

**URL:** <https://discourse.slicer.org/t/segmentation-problem-with-mri-geometric-issues/15899>\
**Category:** Support\
**Created:** [February 8, 2021, 11:28am UTC](https://discourse.slicer.org/t/segmentation-problem-with-mri-geometric-issues/15899 "2021-02-08T11:28:16Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![hao](https://avatars.discourse-cdn.com/v4/letter/h/ea5d25/32.png) [@hao](https://discourse.slicer.org/u/hao)\
**Post date:** [February 8, 2021, 11:28am UTC](https://discourse.slicer.org/t/segmentation-problem-with-mri-geometric-issues/15899/1 "2021-02-08T11:28:16Z")

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Hi, I tried to do segmentation with MRI serie, at import moment, slice give a message of "Geometric issue, images are not equally spaced). I have used transform option of dicom plugin configuartion. But each time I paint with “draw”, there are always the parasite image in the nexte slice.  
Can anyone help me?  
thank you.

 ![slicer_contourage_01.PNG](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/2/2/22b1b1290f43ff9ca2483440d2765bcc835f98b0.jpeg)  
 ![slicer_contourage_02.PNG](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/9/99e2b06fdde59676f6d3b0f68eb2fe7032a1283e.jpeg)

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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:** [February 8, 2021, 3:46pm UTC](https://discourse.slicer.org/t/segmentation-problem-with-mri-geometric-issues/15899/2 "2021-02-08T15:46:40Z")

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> [@hao](#):
>
> transform option of dicom plugin configuartion

This creates a nonlinear transform to correct the scan geometry, so you probably need to [harden this](https://slicer.readthedocs.io/en/latest/user_guide/modules/transforms.html#harden-transform-on-a-node) before you do the segmentation.

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**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:** [February 8, 2021, 7:41pm UTC](https://discourse.slicer.org/t/segmentation-problem-with-mri-geometric-issues/15899/3 "2021-02-08T19:41:35Z")

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In addition to that, it may be possible that the volume axes are not aligned with default slice axes. You may just need to click the warning icon next to the segmentation node selector. See more information [here](https://lassoan.github.io/SlicerSegmentationRecipes/ObliqueSliceSegmentation/).

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**Author:** ![hao](https://avatars.discourse-cdn.com/v4/letter/h/ea5d25/32.png) [@hao](https://discourse.slicer.org/u/hao)\
**Post date:** [February 9, 2021, 4:05pm UTC](https://discourse.slicer.org/t/segmentation-problem-with-mri-geometric-issues/15899/4 "2021-02-09T16:05:17Z")

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thank you lassoan and steve pieper,  
I think my problem is mainly due of the non-aligned volume axe. it is resolved by click the botton beside the segmentation as indicated by the article.  
I have succefully transform all of the segmentation of 2nd CT scan after an important changement morphologique. it’s really fantastique and amazing. I think that we can use 3D slicer for routine traitement.  
before registation, 1er scan vs 2er scan, the segmentations are based on 1er scan

 ![Screenshot from 2021-02-09 15-45-05](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/2/5/258df625d82e57e51193605d1968f52d74862cdd.png)  
two scans without segmentations  
 ![Screenshot from 2021-02-09 15-46-44](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/f/9f65e3e1510cdbcdc771ad70bc5e98360904ebaa.jpeg)  
After rigid segmentation (General registration brain)  
 ![Screenshot from 2021-02-09 15-54-10](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/0/0007049304c52c1d8a973985fb6a1a3a5863da79.jpeg)  
After Bspine segmentation  
 ![Screenshot from 2021-02-09 16-06-09](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/8/0818018b6c352fd7a595d869126f46bacdb45bfd.jpeg)  
the segmentation before application of transform  
 ![Screenshot from 2021-02-09 16-08-21](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/7/576d25cba0b81251024912f3dafddbb54bb04226.jpeg)  
the final position and transformation of the segmentations  
 ![Screenshot from 2021-02-09 16-11-32](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/5/95ca2324d56372da580e47c82d00ccd7ab374a3d.jpeg)

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**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:** [February 9, 2021, 4:40pm UTC](https://discourse.slicer.org/t/segmentation-problem-with-mri-geometric-issues/15899/5 "2021-02-09T16:40:26Z")

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This looks awesome, thanks for sharing!

It would be nice if you could post a few sentences (and maybe 1-2 nice images) in a new topic in [“Success stories”](https://discourse.slicer.org/c/community/success-stories/29) category describing who you are and how 3D Slicer and the community helped you to achieve what you needed. It would help us securing more grant funding to further improve Slicer. Thank you!

> **[Success stories](https://discourse.slicer.org/c/community/success-stories/29)**
>
> This is the place where you can share how Slicer helped your work. Describe your project and how Slicer was useful in achieving your goal. Include reference to any publication(s) and if possible also add a few nice images or links to videos.

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**Author:** ![hao](https://avatars.discourse-cdn.com/v4/letter/h/ea5d25/32.png) [@hao](https://discourse.slicer.org/u/hao)\
**Post date:** [February 9, 2021, 5:42pm UTC](https://discourse.slicer.org/t/segmentation-problem-with-mri-geometric-issues/15899/6 "2021-02-09T17:42:41Z")

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OK, i will do it as soon as possible.  
thank you