# Subrachnoid space segmentation

**URL:** <https://discourse.slicer.org/t/subrachnoid-space-segmentation/14626>\
**Category:** Support\
**Created:** [November 16, 2020, 4:35am UTC](https://discourse.slicer.org/t/subrachnoid-space-segmentation/14626 "2020-11-16T04:35:33Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Vytenis\_R](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/vytenis_r/32/8848_2.png) [@Vytenis\_R](https://discourse.slicer.org/u/Vytenis_R)\
**Post date:** [November 16, 2020, 4:35am UTC](https://discourse.slicer.org/t/subrachnoid-space-segmentation/14626/1 "2020-11-16T04:35:33Z")

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Hello,  
is there an easy way to segment brain subarachnoid space? When I use “Threshold” too many other parts are included.

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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 16, 2020, 7:16am UTC](https://discourse.slicer.org/t/subrachnoid-space-segmentation/14626/2 "2020-11-16T07:16:18Z")

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There are many tools that can help, but the first I would recommend to try is [Local thresholding](https://discourse.slicer.org/t/new-segment-editor-effect-local-threshold/9233) (provided by SegmentEditorExtraEffects extension). You can set a threshold range (optionally an additional region of interest), and then segment a structure by a single click (Ctrl+Left-click).

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**Author:** ![Vytenis\_R](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/vytenis_r/32/8848_2.png) [@Vytenis\_R](https://discourse.slicer.org/u/Vytenis_R)\
**Post date:** [November 22, 2020, 4:09pm UTC](https://discourse.slicer.org/t/subrachnoid-space-segmentation/14626/3 "2020-11-22T16:09:01Z")

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With Local thersholding still too many unwanted areas are selected, maybe I’m doing something wrong? Or there is another way to segment subarachnoid space?

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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 22, 2020, 4:37pm UTC](https://discourse.slicer.org/t/subrachnoid-space-segmentation/14626/4 "2020-11-22T16:37:30Z")

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Local thresholding should work very well for this. Most important is to set the right threshold range. You can enforce further spatial smoothness by choosing watershed mode. You can also set the minimum connecting bridge size to prevent leaking.