Segmentation problem with MRI (geometric issues)

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.

This creates a nonlinear transform to correct the scan geometry, so you probably need to harden this before you do the segmentation.

1 Like

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.

1 Like

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

two scans without segmentations

After rigid segmentation (General registration brain)

After Bspine segmentation

the segmentation before application of transform

the final position and transformation of the segmentations

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” 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!

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