# Skull stripping/ Brain Extraction for canine brains with HDBrainExtraction a/o SwissSkullStripper

**URL:** <https://discourse.slicer.org/t/skull-stripping-brain-extraction-for-canine-brains-with-hdbrainextraction-a-o-swissskullstripper/41472>\
**Category:** Support\
**Tags:** segmentation, swissskullstripper\
**Created:** [February 3, 2025, 9:04pm UTC](https://discourse.slicer.org/t/skull-stripping-brain-extraction-for-canine-brains-with-hdbrainextraction-a-o-swissskullstripper/41472 "2025-02-03T21:04:47Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![ma\_apan](https://avatars.discourse-cdn.com/v4/letter/m/e480ec/32.png) [@ma\_apan](https://discourse.slicer.org/u/ma_apan)\
**Post date:** [February 3, 2025, 9:04pm UTC](https://discourse.slicer.org/t/skull-stripping-brain-extraction-for-canine-brains-with-hdbrainextraction-a-o-swissskullstripper/41472/1 "2025-02-03T21:04:47Z")

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I have to extract canine brains from around 60 patients in T1w 3D MRI-images. I tried both options

- SwissSkullstripper doesn’t extract all brain, but only a small part of the brain (image 1)
- HD Brain Extraction Tool works better, but doesn’t extract all brain as well (image 2)

I tried the HD Brain Extraction Tool with a atlas volume and atlas mask, which I manually segmented beforehand.

image 1: green is the atlas mask segmentation, blue is the brain extraction by Swiss SkullStripping  
image 2: white is brain extraction by HD Brain Extraction

I am thankful for any tipps on how to extract the brain properly or any additional settings that may help. Thanks in advance!

 ![Bildschirmfoto 2025-02-03 um 12.19.54](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/3/9/392d1cbeff3e1d423a1bc85b507162542ecbd675.jpeg)  
 ![image1](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/7/4/74427c7ea303688c2ccdd0754137c5867795735e.jpeg)