# Brain MRI Gray Matter Segmentation

**URL:** <https://discourse.slicer.org/t/brain-mri-gray-matter-segmentation/23718>\
**Category:** Support\
**Created:** [June 5, 2022, 10:33pm UTC](https://discourse.slicer.org/t/brain-mri-gray-matter-segmentation/23718 "2022-06-05T22:33:16Z")\
**Posts on this page:** 1\
**Showing post:** 18

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**Author:** ![drnoorfatima](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/drnoorfatima/32/81980_2.png) [@drnoorfatima](https://discourse.slicer.org/u/drnoorfatima)\
**Post date:** [February 17, 2026, 8:56am UTC](https://discourse.slicer.org/t/brain-mri-gray-matter-segmentation/23718/18 "2026-02-17T08:56:22Z")

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> [@klippert](#):
>
> Dear Community,
> 
> I’m just a 3d printing nerd looking to print my brain from MRI/DCOM files. I’ve been able to extract my brain using HD-BET and Swiss Skull Stripper. Now I’m trying to just isolate the gray matter/cerebral cortex/folds, etc. However, when I use thresholding in segment editor on the extracted brain segment, I can’t seem to get the structure definition on the sides/rear (too smooth) of my brain as shown in the pics.
> 
> If anyone has a step by step tutorial I would greatly appreciated it. I’m just trying to develop a recipe to 3d print brains for myself and family.
> 
> I found a brain logistic segmentation extension in the attached pic. This appears to isolate gray/white matter in 3d slicer, but not sure how to install it? I don’t see it in the list of extensions inside 3d slicer, but I guess there is a way to download the python files, but not that familiar with how to install manually and what sub directory to add it to?
> 
> Any help would be appreciated.
> 
> Thanks,  
> Kurt

Hi Kurt, what a cool project!

The smoothness issue you’re seeing on the sides and rear is actually a really common frustration with this workflow, thresholding alone isn’t designed to capture cortical surface detail well, especially the sulci and gyri. It’s not something you can fix just by adjusting the threshold values.

Getting the cortical folds to come out properly for 3D printing involves a few extra steps beyond what most tutorials cover, and the extension route you found has some compatibility nuances that trip people up.

I work with brain MRI segmentation and have done similar pipelines before. If you want I can take a look at what you have and point you in the right direction, feel free to DM me.

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