# I cannot remove "ridges" in 3D segmentation

**URL:** https://discourse.slicer.org/t/i-cannot-remove-ridges-in-3d-segmentation/4792
**Category:** Support
**Tags:** segmentation
**Created:** [November 19, 2018, 4:07am UTC](https://discourse.slicer.org/t/i-cannot-remove-ridges-in-3d-segmentation/4792 "2018-11-19T04:07:19Z")
**Posts on this page:** 1
**Showing post:** 2

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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: [November 19, 2018, 5:08am UTC](https://discourse.slicer.org/t/i-cannot-remove-ridges-in-3d-segmentation/4792/2 "2018-11-19T05:08:58Z")

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> [@nwskelley](#):
>
> The CT DICOMs I’m using have high resolution cuts in axial, sagittal, and coronal planes, but 3D slicer is making me pick one for the master volume for segmenting.

Unfortunately, this is a common image acquisition problem. See for example [this discussion](https://discourse.slicer.org/t/combining-volumes-what-am-i-missing/2941/2). Maybe imaging techs don’t know that such scans are not well suited for 3D reconstruction or high-resolution 3D reconstruction is not a priority.

Anyway, you can address this by forcing the segmentation’s internal labelmap representation to have isotropic voxel spacing.

Example: Bone segmentation with thresholding. 3D surface representation is created with surface smoothing disabled, master volume’s interpolation is disabled to see voxel boundaries more clearly.

Using the master volume’s spacing (0.7 x 0.7 x 2.5):

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/4/d42ff3b313e0b7c866a456eb0434dbe78cffdfd6.png)

Enable “Isotropic spacing” in the segmentation geometry window (resulting spacing: 0.7 x 0.7 x 0.7) and then re-thresholding (see how blocky the master volume is and how smooth the segmentation(:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/3/b/3bf540d03f2886ffa3322ec1e431dafbf72e2551.png)

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/d/6d2f3bfa14d9cd290c058d28dc511a986d3da7c4.png)

After applying Smoothing effect (method: Closing; Kernel size: 5x5x5 pixels) and enabling surface smoothing (factor=0.5):

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/9/498300db41d39e41ba8198efeef46681d6698b59.png)

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